Zc3h11a (zinc finger CCCH-type containing 11A) - Rat Genome Database

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Gene: Zc3h11a (zinc finger CCCH-type containing 11A) Rattus norvegicus
Analyze
Symbol: Zc3h11a
Name: zinc finger CCCH-type containing 11A
RGD ID: 1308290
Description: Predicted to have mRNA binding activity. Predicted to be involved in poly(A)+ mRNA export from nucleus. Predicted to colocalize with transcription export complex. Orthologous to human ZC3H11A (zinc finger CCCH-type containing 11A); INTERACTS WITH bisphenol A; copper atom; copper(0).
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: hypothetical protein LOC360845; LOC360845; RGD1308290; similar to RIKEN cDNA 5730454B08; zinc finger CCCH domain-containing protein 11A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21345,073,422 - 45,113,901 (-)NCBI
Rnor_6.0 Ensembl1350,196,042 - 50,234,862 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01350,196,042 - 50,234,862 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01355,250,291 - 55,288,525 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41346,546,434 - 46,585,149 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11346,560,476 - 46,599,192 (-)NCBI
Celera1345,407,342 - 45,445,945 (-)NCBICelera
Cytogenetic Map13q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:22658674   PMID:22681889   PMID:22928037  


Genomics

Comparative Map Data
Zc3h11a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21345,073,422 - 45,113,901 (-)NCBI
Rnor_6.0 Ensembl1350,196,042 - 50,234,862 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01350,196,042 - 50,234,862 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01355,250,291 - 55,288,525 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41346,546,434 - 46,585,149 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11346,560,476 - 46,599,192 (-)NCBI
Celera1345,407,342 - 45,445,945 (-)NCBICelera
Cytogenetic Map13q13NCBI
ZC3H11A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1203,795,623 - 203,854,999 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1203,795,714 - 203,854,999 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1203,795,654 - 203,854,999 (+)EnsemblGRCh38hg38GRCh38
GRCh381203,795,623 - 203,854,126 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371203,764,751 - 203,823,252 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361202,031,374 - 202,089,879 (+)NCBINCBI36hg18NCBI36
Celera1176,894,976 - 176,957,901 (+)NCBI
Cytogenetic Map1q32.1NCBI
HuRef1174,930,259 - 174,989,504 (+)NCBIHuRef
CHM1_11205,188,206 - 205,246,806 (+)NCBICHM1_1
Zc3h11a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391133,547,600 - 133,589,137 (-)NCBIGRCm39mm39
GRCm39 Ensembl1133,547,600 - 133,589,118 (-)Ensembl
GRCm39 Ensembl1133,547,609 - 133,589,118 (-)Ensembl
GRCm381133,619,862 - 133,661,399 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1133,619,871 - 133,661,380 (-)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl1133,619,862 - 133,661,380 (-)EnsemblGRCm38mm10GRCm38
MGSCv371135,516,448 - 135,557,957 (-)NCBIGRCm37mm9NCBIm37
MGSCv361135,449,041 - 135,482,553 (-)NCBImm8
Celera1136,233,840 - 136,276,673 (-)NCBICelera
Cytogenetic Map1E4NCBI
Zc3h11a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540639,678,544 - 39,718,062 (+)NCBIChiLan1.0ChiLan1.0
ZC3H11A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11183,689,698 - 183,747,943 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01179,399,533 - 179,458,811 (+)NCBIMhudiblu_PPA_v0panPan3
ZC3H11A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.138477,900 - 505,754 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha38556,158 - 601,505 (+)NCBI
ROS_Cfam_1.038456,184 - 501,695 (+)NCBI
UMICH_Zoey_3.138453,063 - 498,400 (+)NCBI
UNSW_CanFamBas_1.038843,427 - 888,688 (+)NCBI
UU_Cfam_GSD_1.0381,057,617 - 1,103,068 (+)NCBI
Zc3h11a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934471,628,681 - 71,652,940 (-)NCBI
SpeTri2.0NW_004936567863,295 - 901,837 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZC3H11A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1964,518,895 - 64,554,871 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2970,867,408 - 70,903,386 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ZC3H11A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12525,490,837 - 25,548,262 (-)NCBI
Vero_WHO_p1.0NW_02366605526,265,336 - 26,323,003 (-)NCBI
Zc3h11a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248077,099,539 - 7,165,450 (-)NCBI

Position Markers
BE120749  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21345,112,025 - 45,112,222 (-)MAPPER
Rnor_6.01350,197,721 - 50,197,917NCBIRnor6.0
Rnor_5.01355,251,833 - 55,252,029UniSTSRnor5.0
RGSC_v3.41346,583,371 - 46,583,567UniSTSRGSC3.4
Celera1345,444,199 - 45,444,395UniSTS
RH 3.4 Map13173.9UniSTS
Cytogenetic Map13q13UniSTS
RH137294  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map13q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
61339Bp24Blood pressure QTL 240.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13901674250513953Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131409633059096330Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131409633059096330Rat
1300163Cardf1Cardiac cell morphology QTL 14.18aorta morphology trait (VT:0000272)artery lesion measurement (CMO:0000975)131444158250799665Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131444158251577031Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131981081464810814Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)132005247765052477Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132148248158537177Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132800833873008338Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132858445273584452Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132907693474076934Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132907693474076934Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133614753364868393Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133734634882346348Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133937292784372927Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)134231074486833540Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)134231074487310744Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134357571788575717Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
2303032Bp328Blood pressure QTL 328arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134644457050799665Rat
4145117Mcs27Mammary carcinoma susceptibility QTL 270.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)134877665553264877Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134905850767207219Rat
12879436Bp395Blood pressure QTL 395arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134999470851081193Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:46
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000004025
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 42 57 41 19 41 8 11 74 35 41 11 8
Low 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001047902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090892 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC105642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC088342 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC111404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC161921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ480752 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000090858   ⟹   ENSRNOP00000071151
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1350,196,042 - 50,234,862 (+)Ensembl
RefSeq Acc Id: NM_001047902   ⟹   NP_001041367
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21345,075,077 - 45,113,901 (-)NCBI
Rnor_6.01350,196,042 - 50,234,862 (+)NCBI
Rnor_5.01355,250,291 - 55,288,525 (+)NCBI
RGSC_v3.41346,546,434 - 46,585,149 (-)RGD
Celera1345,407,342 - 45,445,945 (-)RGD
Sequence:
RefSeq Acc Id: XM_039090891   ⟹   XP_038946819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21345,073,422 - 45,113,277 (-)NCBI
RefSeq Acc Id: XM_039090892   ⟹   XP_038946820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21345,073,422 - 45,106,789 (-)NCBI
RefSeq Acc Id: XM_039090893   ⟹   XP_038946821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21345,074,637 - 45,107,035 (-)NCBI
RefSeq Acc Id: XM_039090894   ⟹   XP_038946822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21345,073,422 - 45,098,318 (-)NCBI
RefSeq Acc Id: XM_039090895   ⟹   XP_038946823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21345,073,422 - 45,106,789 (-)NCBI
RefSeq Acc Id: XM_039090896   ⟹   XP_038946824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21345,073,422 - 45,089,114 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001041367   ⟸   NM_001047902
- UniProtKB: Q0ZFS5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071151   ⟸   ENSRNOT00000090858
RefSeq Acc Id: XP_038946819   ⟸   XM_039090891
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946823   ⟸   XM_039090895
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038946820   ⟸   XM_039090892
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946822   ⟸   XM_039090894
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038946824   ⟸   XM_039090896
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038946821   ⟸   XM_039090893
- Peptide Label: isoform X3
Protein Domains
C3H1-type

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13698822
Promoter ID:EPDNEW_R9346
Type:initiation region
Name:Zc3h11a_1
Description:zinc finger CCCH-type containing 11A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01350,196,012 - 50,196,072EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 50198367 50198368 T C snv WKY/N (MCW)
13 50198369 50198370 A G snv WKY/NCrl (RGD), COP/CrCrl (MCW & UW), GK/Ox (RGD), WKY/NHsd (RGD)
13 50198872 50198873 A T snv F344/NRrrc (MCW)
13 50199631 50199632 A C snv LEW/NCrlBR (RGD)
13 50215990 50215991 A G snv CDS
13 50216065 50216066 G A snv CDR, SBH/Ygl (MCW), ACI/EurMcwi (MCW), CDS, GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), SR/JrHsd (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW)
13 50216116 50216117 C T snv FHL/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), CDS, CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW)
13 50228835 50228836 G A snv CDR
13 50229162 50229163 C A snv SBH/Ygl (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), GH/OmrMcwi (MCW)
13 50231392 50231393 G T snv SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), GH/OmrMcwi (MCW), CDS, ACI/EurMcwi (MCW), CDR
13 50234852 50234853 T C snv CDS, SBN/Ygl (MCW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), SR/JrHsd (MCW), CDR, SBH/Ygl (MCW), SS/JrHsdMcwi (MCW), GH/OmrMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 46546612 46546613 G T snv SHRSP/Gcrc (MDC)
13 46549896 46549897 C A snv ACI/N (KNAW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), F344/NRrrc (KNAW), LE/Stm (KNAW), M520/N (KNAW), MR/N (KNAW), WN/N (KNAW), ACI/EurMcwi (MCW)
13 46552126 46552127 G T snv LE/Stm (ICL), SR/JrHsd (MCW), GH/OmrMcwi (MCW), SBN/Ygl (ICL), SBH/Ygl (ICL), SS/JrHsdMcwi (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308290 AgrOrtholog
Ensembl Genes ENSRNOG00000053210 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071151 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000090858 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7373975 IMAGE-MGC_LOAD
InterPro Znf-CCCH_3 UniProtKB/TrEMBL
  Znf_CCCH UniProtKB/TrEMBL
KEGG Report rno:360845 UniProtKB/TrEMBL
MGC_CLONE MGC:125178 IMAGE-MGC_LOAD
NCBI Gene 360845 ENTREZGENE
Pfam zf-CCCH_3 UniProtKB/TrEMBL
PhenoGen Zc3h11a PhenoGen
PROSITE ZF_C3H1 UniProtKB/TrEMBL
SMART ZnF_C3H1 UniProtKB/TrEMBL
UniProt Q0ZFS5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Zc3h11a  zinc finger CCCH-type containing 11A  RGD1308290  similar to RIKEN cDNA 5730454B08  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1308290  similar to RIKEN cDNA 5730454B08   RGD1308290_predicted  similar to RIKEN cDNA 5730454B08 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1308290_predicted  similar to RIKEN cDNA 5730454B08 (predicted)  LOC360845_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC360845_predicted  similar to RIKEN cDNA 5730454B08 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL