Rogdi (rogdi homolog) - Rat Genome Database

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Gene: Rogdi (rogdi homolog) Mus musculus
Analyze
Symbol: Rogdi
Name: rogdi homolog
RGD ID: 1615906
MGI Page MGI
Description: Acts upstream of or within several processes, including enamel mineralization; locomotor rhythm; and pH reduction. Predicted to be located in nuclear envelope. Predicted to be part of RAVE complex. Predicted to be active in hippocampal mossy fiber to CA3 synapse and presynapse. Is expressed in several structures, including central nervous system; genitourinary system; nose; spinal ganglion; and tooth. Used to study Kohlschutter-Tonz syndrome. Human ortholog(s) of this gene implicated in Kohlschutter-Tonz syndrome. Orthologous to human ROGDI (rogdi atypical leucine zipper).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 0610011C19Rik; AU020118; C76152; leucine zipper domain protein; leucine-zipper-containing LZF; Lz; Lzf; protein rogdi homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39164,826,593 - 4,831,438 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl164,826,594 - 4,831,417 (-)EnsemblGRCm39 Ensembl
GRCm38165,008,729 - 5,013,574 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl165,008,730 - 5,013,553 (-)EnsemblGRCm38mm10GRCm38
MGSCv37165,008,822 - 5,013,646 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36164,924,066 - 4,928,840 (-)NCBIMGSCv36mm8
Celera165,640,103 - 5,644,927 (-)NCBICelera
Cytogenetic Map16A1NCBI
cM Map162.49NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10725249   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11740862   PMID:12438443   PMID:12466851   PMID:12477932   PMID:15582152  
PMID:15618518   PMID:15782199   PMID:16141072   PMID:16141073   PMID:16512683   PMID:16602821   PMID:16959763   PMID:20412781   PMID:21267068   PMID:21873635   PMID:32581705   PMID:38172607  


Genomics

Comparative Map Data
Rogdi
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39164,826,593 - 4,831,438 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl164,826,594 - 4,831,417 (-)EnsemblGRCm39 Ensembl
GRCm38165,008,729 - 5,013,574 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl165,008,730 - 5,013,553 (-)EnsemblGRCm38mm10GRCm38
MGSCv37165,008,822 - 5,013,646 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36164,924,066 - 4,928,840 (-)NCBIMGSCv36mm8
Celera165,640,103 - 5,644,927 (-)NCBICelera
Cytogenetic Map16A1NCBI
cM Map162.49NCBI
ROGDI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38164,796,968 - 4,802,633 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl164,796,968 - 4,802,880 (-)EnsemblGRCh38hg38GRCh38
GRCh37164,846,969 - 4,852,634 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36164,786,970 - 4,792,675 (-)NCBINCBI36Build 36hg18NCBI36
Celera165,055,739 - 5,061,444 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef164,813,161 - 4,819,149 (-)NCBIHuRef
CHM1_1164,847,809 - 4,853,797 (-)NCBICHM1_1
T2T-CHM13v2.0164,826,450 - 4,832,187 (-)NCBIT2T-CHM13v2.0
Rogdi
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81011,074,288 - 11,078,907 (+)NCBIGRCr8
mRatBN7.21010,567,834 - 10,572,453 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1010,567,834 - 10,572,452 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1015,275,819 - 15,280,438 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01014,764,638 - 14,769,257 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01010,433,931 - 10,438,567 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01010,761,477 - 10,766,096 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1010,761,477 - 10,766,095 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0109,528,490 - 9,533,109 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41010,683,729 - 10,688,348 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera109,531,610 - 9,536,229 (+)NCBICelera
Cytogenetic Map10q12NCBI
Rogdi
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544212,694,197 - 12,700,181 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544212,694,197 - 12,700,181 (+)NCBIChiLan1.0ChiLan1.0
ROGDI
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2185,325,112 - 5,331,145 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1169,115,264 - 9,121,257 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0163,721,063 - 3,727,056 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1164,886,553 - 4,892,611 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl164,887,051 - 4,892,607 (-)Ensemblpanpan1.1panPan2
ROGDI
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1636,618,670 - 36,624,533 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl636,491,561 - 36,624,532 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha638,010,765 - 38,016,786 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0636,821,485 - 36,827,506 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl636,820,987 - 36,827,503 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1636,615,541 - 36,621,550 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0636,508,424 - 36,514,446 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0636,910,640 - 36,916,661 (+)NCBIUU_Cfam_GSD_1.0
Rogdi
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344106,910,628 - 106,916,187 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365304,753,751 - 4,761,695 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365304,756,069 - 4,761,484 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ROGDI
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl337,591,815 - 37,602,112 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1337,592,982 - 37,600,004 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2338,665,099 - 38,671,065 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ROGDI
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.154,466,954 - 4,472,967 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl54,466,824 - 4,472,780 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606826,186,555 - 26,192,558 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rogdi
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248242,650,116 - 2,655,716 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248242,649,694 - 2,655,728 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rogdi
152 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:364
Count of miRNA genes:285
Interacting mature miRNAs:302
Transcripts:ENSMUST00000023191, ENSMUST00000090453
Prediction methods: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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301970Heal11_mwound healing/regeneration 11 (mouse)Not determined16124263853Mouse
4141468Nhdlq10_mnon-HDL QTL 10 (mouse)Not determined16124263853Mouse
1301559Bbaa19_mB.burgdorferi-associated arthritis 19 (mouse)Not determined16130066977Mouse
38501069Tip4_mtuberculosis immunophenotype 4, IFN-g level (mouse)16431786444520363Mouse
1302106Rapop1_mradiation-induced apoptosis 1 (mouse)Not determined16378077915731053Mouse
26884432Zlq7_mzygomatic length QTL 7, 10 week (mouse)16381786464620363Mouse
1300632Loca2_mlocomotor activity 2 (mouse)Not determined16122500574Mouse
27226768Tibl9_mtibia length 9, 5 week (mouse)16331786451420363Mouse
1301443Mopkd2_mmodifier of polycystic kidney disease progression 2 (mouse)Not determined16464631438646414Mouse
1301575Tanidd3_mtally ho associated non-insulin dependednt diabetes mellitus 3 (mouse)Not determined16122897739Mouse
27095908Scvln7_msacral vertebrae length 2, 5 week (mouse)16331786439820362Mouse
4141060Pbwg19_mpostnatal body weight growth 19 (mouse)Not determined16120780888Mouse
1301384Dice1_mdetermination of interleukin 4 commitment 1 (mouse)Not determined16128434358Mouse
10043879Adip25_madiposity 25 (mouse)Not determined16122520318Mouse
27226785Feml12_mfemur length 12, 5 week (mouse)16331786464620363Mouse
10402497Lmr23_mleishmaniasis resistance 23 (mouse)Not determined16129674200Mouse
10412289Ppsl_mplasma P-selectin levels (mouse)Not determined16130814572Mouse

Markers in Region
RH136355  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38165,008,764 - 5,008,965UniSTSGRCm38
MGSCv37165,008,857 - 5,009,058UniSTSGRCm37
Celera165,640,138 - 5,640,339UniSTS
Cytogenetic Map16A1UniSTS
cM Map163.3UniSTS
AW545332  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38165,014,321 - 5,014,438UniSTSGRCm38
MGSCv37165,014,414 - 5,014,531UniSTSGRCm37
Celera165,645,695 - 5,645,812UniSTS
Cytogenetic Map16A1UniSTS
cM Map163.4UniSTS
cM Map163.3UniSTS
C76152  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38165,008,857 - 5,008,996UniSTSGRCm38
MGSCv37165,008,950 - 5,009,089UniSTSGRCm37
Celera165,640,231 - 5,640,370UniSTS
Cytogenetic Map16A1UniSTS
cM Map163.3UniSTS
Whitehead/MRC_RH1621.2UniSTS
0610011C19Rik  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map16A1UniSTS
cM Map163.3UniSTS
cM Map16 UniSTS
cM MapUN UniSTS
UniSTS:237418  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38165,014,326 - 5,014,576UniSTSGRCm38
MGSCv37165,014,419 - 5,014,669UniSTSGRCm37
Celera165,645,700 - 5,645,950UniSTS
Cytogenetic Map16A1UniSTS
cM Map163.4UniSTS
cM Map163.3UniSTS


Sequence


Ensembl Acc Id: ENSMUST00000023191   ⟹   ENSMUSP00000023191
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,826,594 - 4,831,391 (-)Ensembl
GRCm38.p6 Ensembl165,008,730 - 5,013,527 (-)Ensembl
Ensembl Acc Id: ENSMUST00000090453   ⟹   ENSMUSP00000087938
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,826,619 - 4,831,381 (-)Ensembl
GRCm38.p6 Ensembl165,008,755 - 5,013,517 (-)Ensembl
Ensembl Acc Id: ENSMUST00000201077   ⟹   ENSMUSP00000144166
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,828,721 - 4,831,349 (-)Ensembl
GRCm38.p6 Ensembl165,010,857 - 5,013,485 (-)Ensembl
Ensembl Acc Id: ENSMUST00000201118
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,827,772 - 4,829,689 (-)Ensembl
GRCm38.p6 Ensembl165,009,908 - 5,011,825 (-)Ensembl
Ensembl Acc Id: ENSMUST00000201651
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,829,573 - 4,831,417 (-)Ensembl
GRCm38.p6 Ensembl165,011,709 - 5,013,553 (-)Ensembl
Ensembl Acc Id: ENSMUST00000201726
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,826,849 - 4,828,525 (-)Ensembl
GRCm38.p6 Ensembl165,008,985 - 5,010,661 (-)Ensembl
Ensembl Acc Id: ENSMUST00000202281   ⟹   ENSMUSP00000144481
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,826,594 - 4,831,381 (-)Ensembl
GRCm38.p6 Ensembl165,008,730 - 5,013,517 (-)Ensembl
Ensembl Acc Id: ENSMUST00000202640
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,827,088 - 4,827,982 (-)Ensembl
GRCm38.p6 Ensembl165,009,224 - 5,010,118 (-)Ensembl
Ensembl Acc Id: ENSMUST00000202720
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,827,909 - 4,829,605 (-)Ensembl
GRCm38.p6 Ensembl165,010,045 - 5,011,741 (-)Ensembl
Ensembl Acc Id: ENSMUST00000202998
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl164,830,034 - 4,831,400 (-)Ensembl
GRCm38.p6 Ensembl165,012,170 - 5,013,536 (-)Ensembl
RefSeq Acc Id: NM_133185   ⟹   NP_573448
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39164,826,593 - 4,831,417 (-)NCBI
GRCm38165,008,729 - 5,013,553 (-)NCBI
MGSCv37165,008,822 - 5,013,646 (-)RGD
Celera165,640,103 - 5,644,927 (-)RGD
cM Map16 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_036160082   ⟹   XP_036015975
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39164,827,844 - 4,831,438 (-)NCBI
Sequence:
RefSeq Acc Id: XR_004939203
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39164,826,594 - 4,831,438 (-)NCBI
Sequence:
RefSeq Acc Id: NP_573448   ⟸   NM_133185
- UniProtKB: Q922N4 (UniProtKB/Swiss-Prot),   Q8BL37 (UniProtKB/Swiss-Prot),   Q923H8 (UniProtKB/Swiss-Prot),   Q3TDK6 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000087938   ⟸   ENSMUST00000090453
Ensembl Acc Id: ENSMUSP00000144481   ⟸   ENSMUST00000202281
Ensembl Acc Id: ENSMUSP00000023191   ⟸   ENSMUST00000023191
Ensembl Acc Id: ENSMUSP00000144166   ⟸   ENSMUST00000201077
RefSeq Acc Id: XP_036015975   ⟸   XM_036160082
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3TDK6-F1-model_v2 AlphaFold Q3TDK6 1-287 view protein structure

Promoters
RGD ID:6827420
Promoter ID:MM_KWN:20011
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:ES_Cell,   Kidney,   Lung
Transcripts:UC007YBJ.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36165,012,409 - 5,012,909 (-)MPROMDB
RGD ID:6827421
Promoter ID:MM_KWN:20012
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000023191,   ENSMUST00000090453,   NM_133185
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36165,013,346 - 5,014,527 (-)MPROMDB
RGD ID:8685416
Promoter ID:EPDNEW_M20714
Type:initiation region
Name:Rogdi_1
Description:Mus musculus rogdi homolog , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38165,013,521 - 5,013,581EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1913299 AgrOrtholog
Ensembl Genes ENSMUSG00000022540 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000023191.17 UniProtKB/Swiss-Prot
  ENSMUST00000201077.2 UniProtKB/TrEMBL
  ENSMUST00000202281 ENTREZGENE
  ENSMUST00000202281.4 UniProtKB/Swiss-Prot
InterPro RAVE2/Rogdi UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:66049 UniProtKB/Swiss-Prot
MGD MGI:1913299 ENTREZGENE
NCBI Gene 66049 ENTREZGENE
PANTHER PROTEIN ROGDI HOMOLOG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13618 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Rogdi_lz UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rogdi PhenoGen
UniProt A0A0J9YUG1_MOUSE UniProtKB/TrEMBL
  Q3TDK6 ENTREZGENE
  Q8BL37 ENTREZGENE
  Q922N4 ENTREZGENE
  Q923H8 ENTREZGENE
  ROGDI_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q8BL37 UniProtKB/Swiss-Prot
  Q922N4 UniProtKB/Swiss-Prot
  Q923H8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-29 Rogdi  rogdi homolog    rogdi homolog (Drosophila)  Symbol and/or name change 5135510 APPROVED