Eaf1 (ELL associated factor 1) - Rat Genome Database

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Gene: Eaf1 (ELL associated factor 1) Rattus norvegicus
Analyze
Symbol: Eaf1
Name: ELL associated factor 1
RGD ID: 1310057
Description: Predicted to enable transcription elongation factor activity. Predicted to be involved in regulation of transcription elongation by RNA polymerase II and transcription elongation by RNA polymerase II. Predicted to be located in intercellular bridge and nuclear body. Predicted to be part of transcription elongation factor complex. Orthologous to human EAF1 (ELL associated factor 1); PARTICIPATES IN RNA polymerase II transcription elongation pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ELL-associated factor 1; LOC306261
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2166,698,322 - 6,713,071 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl166,698,322 - 6,713,071 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx166,710,831 - 6,725,457 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0167,855,725 - 7,870,351 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0166,718,496 - 6,733,172 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0167,588,217 - 7,602,966 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl167,588,217 - 7,602,966 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0167,523,081 - 7,537,830 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4166,938,938 - 6,953,687 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1166,939,794 - 6,950,565 (+)NCBI
Celera168,477,375 - 8,492,124 (-)NCBICelera
Cytogenetic Map16p16NCBI
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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. The super elongation complex (SEC) family in transcriptional control. Luo Z, etal., Nat Rev Mol Cell Biol. 2012 Sep;13(9):543-7. doi: 10.1038/nrm3417. Epub 2012 Aug 16.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:22195968  


Genomics

Comparative Map Data
Eaf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2166,698,322 - 6,713,071 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl166,698,322 - 6,713,071 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx166,710,831 - 6,725,457 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0167,855,725 - 7,870,351 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0166,718,496 - 6,733,172 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0167,588,217 - 7,602,966 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl167,588,217 - 7,602,966 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0167,523,081 - 7,537,830 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4166,938,938 - 6,953,687 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1166,939,794 - 6,950,565 (+)NCBI
Celera168,477,375 - 8,492,124 (-)NCBICelera
Cytogenetic Map16p16NCBI
EAF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38315,427,598 - 15,442,613 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl315,427,598 - 15,450,635 (+)EnsemblGRCh38hg38GRCh38
GRCh37315,469,105 - 15,484,120 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36315,444,068 - 15,459,124 (+)NCBINCBI36Build 36hg18NCBI36
Build 34315,443,865 - 15,459,123NCBI
Celera315,407,296 - 15,422,352 (+)NCBICelera
Cytogenetic Map3p25.1NCBI
HuRef315,404,403 - 15,419,455 (+)NCBIHuRef
CHM1_1315,419,949 - 15,434,999 (+)NCBICHM1_1
T2T-CHM13v2.0315,430,010 - 15,445,021 (+)NCBIT2T-CHM13v2.0
Eaf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391431,217,036 - 31,231,815 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1431,216,356 - 31,231,815 (+)EnsemblGRCm39 Ensembl
GRCm381431,495,079 - 31,509,858 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1431,494,399 - 31,509,858 (+)EnsemblGRCm38mm10GRCm38
MGSCv371432,308,265 - 32,323,044 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361430,324,152 - 30,338,867 (+)NCBIMGSCv36mm8
Celera1427,754,057 - 27,768,861 (+)NCBICelera
Cytogenetic Map14BNCBI
cM Map1419.14NCBI
Eaf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554301,933,290 - 1,947,932 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554301,933,290 - 1,946,900 (+)NCBIChiLan1.0ChiLan1.0
EAF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1315,417,430 - 15,432,533 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0315,353,459 - 15,368,579 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1315,689,745 - 15,705,300 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl315,689,745 - 15,705,300 (+)Ensemblpanpan1.1panPan2
EAF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12327,188,983 - 27,203,441 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2327,159,751 - 27,203,558 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2327,163,324 - 27,177,930 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02327,701,202 - 27,715,545 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2327,629,445 - 27,715,744 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12327,390,596 - 27,404,986 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02327,452,366 - 27,466,745 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02327,701,137 - 27,715,537 (-)NCBIUU_Cfam_GSD_1.0
Eaf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118169,811,142 - 169,825,002 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364732,949,692 - 2,963,554 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364732,950,321 - 2,963,560 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EAF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl132,654,630 - 2,671,132 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1132,654,829 - 2,671,140 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2132,581,817 - 2,597,145 (+)NCBISscrofa10.2Sscrofa10.2susScr3
EAF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11560,261,013 - 60,277,177 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1560,260,967 - 60,277,626 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604133,293,734 - 33,309,009 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Eaf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248225,239,964 - 5,253,810 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248225,240,423 - 5,253,762 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Eaf1
45 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:579
Count of miRNA genes:252
Interacting mature miRNAs:344
Transcripts:ENSRNOT00000026525
Prediction methods:Microtar, Miranda, Targetscan
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16285170915884239Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760916039848Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat

Markers in Region
AI666536  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2166,712,730 - 6,712,810 (+)MAPPERmRatBN7.2
Rnor_6.0167,602,626 - 7,602,705NCBIRnor6.0
Rnor_5.0167,537,490 - 7,537,569UniSTSRnor5.0
RGSC_v3.4166,953,347 - 6,953,426UniSTSRGSC3.4
Celera168,477,636 - 8,477,715UniSTS
Cytogenetic Map16p16UniSTS


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 22 35 24 18 24 63 34 33 11
Low 21 22 17 1 17 8 11 11 1 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026525   ⟹   ENSRNOP00000026525
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl166,698,322 - 6,713,071 (+)Ensembl
Rnor_6.0 Ensembl167,588,217 - 7,602,966 (+)Ensembl
RefSeq Acc Id: NM_001107293   ⟹   NP_001100763
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,698,322 - 6,713,071 (+)NCBI
Rnor_6.0167,588,217 - 7,602,966 (+)NCBI
Rnor_5.0167,523,081 - 7,537,830 (+)NCBI
RGSC_v3.4166,938,938 - 6,953,687 (+)RGD
Celera168,477,375 - 8,492,124 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100763 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL88944 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000026525
  ENSRNOP00000026525.5
Reference Protein Sequences
RefSeq Acc Id: NP_001100763   ⟸   NM_001107293
- UniProtKB: D4A2G7 (UniProtKB/TrEMBL),   A6KFY7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026525   ⟸   ENSRNOT00000026525
Protein Domains
Transcription elongation factor Eaf N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A2G7-F1-model_v2 AlphaFold D4A2G7 1-355 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310057 AgrOrtholog
BioCyc Gene G2FUF-12145 BioCyc
Ensembl Genes ENSRNOG00000019559 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026525 ENTREZGENE
  ENSRNOT00000026525.6 UniProtKB/TrEMBL
InterPro Eaf_ELL-associated_factor UniProtKB/TrEMBL
  EAF_fam UniProtKB/TrEMBL
KEGG Report rno:306261 UniProtKB/TrEMBL
NCBI Gene 306261 ENTREZGENE
PANTHER ELL-ASSOCIATED FACTOR 1 UniProtKB/TrEMBL
  PTHR15970 UniProtKB/TrEMBL
Pfam EAF UniProtKB/TrEMBL
PhenoGen Eaf1 PhenoGen
RatGTEx ENSRNOG00000019559 RatGTEx
UniProt A6KFY7 ENTREZGENE, UniProtKB/TrEMBL
  D4A2G7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Eaf1  ELL associated factor 1   Eaf1_predicted  ELL associated factor 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Eaf1_predicted  ELL associated factor 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED