Tbc1d25 (TBC1 domain family, member 25) - Rat Genome Database

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Gene: Tbc1d25 (TBC1 domain family, member 25) Rattus norvegicus
Analyze
Symbol: Tbc1d25
Name: TBC1 domain family, member 25
RGD ID: 1559711
Description: Predicted to enable GTPase activator activity. Predicted to be involved in regulation of autophagosome maturation. Predicted to be active in autophagosome. Orthologous to human TBC1D25 (TBC1 domain family member 25); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 2-methoxyethanol; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC302552; Oatl1; ornithine aminotransferase-like 1; RGD1559711; similar to ornithine aminotransferase-like 1; TBC1 domain family member 25
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
GRCr8X16,986,629 - 17,010,228 (+)NCBIGRCr8
mRatBN7.2X14,314,095 - 14,339,171 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX14,314,414 - 14,338,275 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX19,128,166 - 19,151,717 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X20,931,363 - 20,954,913 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X17,196,554 - 17,220,107 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X15,064,733 - 15,088,579 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,064,594 - 15,088,589 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X15,847,845 - 15,871,462 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,346,792 - 26,368,696 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX14,400,116 - 14,423,435 (+)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
autophagosome  (IBA,ISO)

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:21383079   PMID:38100060  


Genomics

Comparative Map Data
Tbc1d25
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X16,986,629 - 17,010,228 (+)NCBIGRCr8
mRatBN7.2X14,314,095 - 14,339,171 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX14,314,414 - 14,338,275 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX19,128,166 - 19,151,717 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X20,931,363 - 20,954,913 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X17,196,554 - 17,220,107 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X15,064,733 - 15,088,579 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,064,594 - 15,088,589 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X15,847,845 - 15,871,462 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,346,792 - 26,368,696 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX14,400,116 - 14,423,435 (+)NCBICelera
Cytogenetic MapXq12NCBI
TBC1D25
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X48,539,714 - 48,562,609 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX48,539,714 - 48,562,609 (+)EnsemblGRCh38hg38GRCh38
GRCh37X48,398,102 - 48,420,997 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,283,019 - 48,305,941 (+)NCBINCBI36Build 36hg18NCBI36
CeleraX53,244,734 - 53,267,656 (-)NCBICelera
Cytogenetic MapXp11.23NCBI
HuRefX46,061,342 - 46,083,902 (+)NCBIHuRef
CHM1_1X48,429,335 - 48,452,245 (+)NCBICHM1_1
T2T-CHM13v2.0X47,948,728 - 47,971,622 (+)NCBIT2T-CHM13v2.0
Tbc1d25
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X8,020,709 - 8,042,420 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX8,020,711 - 8,042,420 (-)EnsemblGRCm39 Ensembl
GRCm38X8,154,470 - 8,176,181 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX8,154,472 - 8,176,181 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X7,731,598 - 7,753,307 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X7,311,438 - 7,333,140 (-)NCBIMGSCv36mm8
CeleraX3,293,890 - 3,314,558 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.69NCBI
Tbc1d25
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543127,162 - 154,235 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955543127,314 - 154,235 (+)NCBIChiLan1.0ChiLan1.0
TBC1D25
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X50,028,529 - 50,051,487 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X50,031,901 - 50,053,471 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X40,837,887 - 40,860,885 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X48,701,734 - 48,724,366 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX48,701,740 - 48,724,366 (+)Ensemblpanpan1.1panPan2
TBC1D25
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X41,782,774 - 41,799,083 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX41,782,671 - 41,798,828 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,158,976 - 16,175,287 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X50,279,318 - 50,294,936 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X41,905,827 - 41,922,129 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X41,894,155 - 41,910,472 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X41,987,718 - 42,004,056 (+)NCBIUU_Cfam_GSD_1.0
Tbc1d25
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,284,015 - 34,296,529 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936721524,247 - 537,363 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936721524,398 - 536,918 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBC1D25
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX42,682,269 - 42,696,574 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X42,682,267 - 42,696,579 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X47,567,160 - 47,584,195 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TBC1D25
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X45,671,217 - 45,691,307 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607611,122,948 - 11,164,441 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tbc1d25
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624893363,688 - 393,301 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624893364,004 - 390,517 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tbc1d25
76 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:210
Count of miRNA genes:147
Interacting mature miRNAs:163
Transcripts:ENSRNOT00000007130
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, 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
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat

Markers in Region
RH144337  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,336,956 - 14,337,098 (+)MAPPERmRatBN7.2
Rnor_6.0X15,087,256 - 15,087,397NCBIRnor6.0
Rnor_5.0X15,870,139 - 15,870,280UniSTSRnor5.0
RGSC_v3.4X26,367,378 - 26,367,519UniSTSRGSC3.4
CeleraX14,422,117 - 14,422,258UniSTS
RH 3.4 MapX127.7UniSTS
Cytogenetic MapXq13UniSTS


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 2 2 2 2 2 60 18 28 3
Low 1 43 55 39 17 39 8 11 14 17 13 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007130   ⟹   ENSRNOP00000007130
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,314,414 - 14,338,275 (+)Ensembl
Rnor_6.0 EnsemblX15,064,594 - 15,088,589 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099656   ⟹   ENSRNOP00000095370
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,316,519 - 14,338,275 (+)Ensembl
RefSeq Acc Id: NM_001106955   ⟹   NP_001100425
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X16,986,629 - 17,010,228 (+)NCBI
mRatBN7.2X14,314,674 - 14,338,275 (+)NCBI
Rnor_6.0X15,064,733 - 15,088,574 (+)NCBI
Rnor_5.0X15,847,845 - 15,871,462 (+)NCBI
RGSC_v3.4X26,346,792 - 26,368,696 (+)RGD
CeleraX14,400,116 - 14,423,435 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256701   ⟹   XP_006256763
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X16,988,419 - 17,010,228 (+)NCBI
mRatBN7.2X14,316,444 - 14,339,171 (+)NCBI
Rnor_6.0X15,066,331 - 15,088,579 (+)NCBI
Rnor_5.0X15,847,845 - 15,871,462 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601993   ⟹   XP_017457482
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X16,988,368 - 17,010,228 (+)NCBI
mRatBN7.2X14,316,413 - 14,339,171 (+)NCBI
Rnor_6.0X15,066,331 - 15,088,579 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063279917   ⟹   XP_063135987
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X16,988,387 - 17,010,228 (+)NCBI
RefSeq Acc Id: XM_063279918   ⟹   XP_063135988
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X16,988,377 - 17,010,228 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001100425   ⟸   NM_001106955
- UniProtKB: B1WBS1 (UniProtKB/TrEMBL),   F7F8Z1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256763   ⟸   XM_006256701
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ALA8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457482   ⟸   XM_017601993
- Peptide Label: isoform X2
- UniProtKB: A0A8I6ALA8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007130   ⟸   ENSRNOT00000007130
RefSeq Acc Id: ENSRNOP00000095370   ⟸   ENSRNOT00000099656
RefSeq Acc Id: XP_063135988   ⟸   XM_063279918
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063135987   ⟸   XM_063279917
- Peptide Label: isoform X3
Protein Domains
Rab-GAP TBC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1WBS1-F1-model_v2 AlphaFold B1WBS1 1-688 view protein structure

Transcriptome

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

Promoters
RGD ID:13701729
Promoter ID:EPDNEW_R12253
Type:multiple initiation site
Name:Tbc1d25_1
Description:TBC1 domain family, member 25
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_6.0X15,064,686 - 15,064,746EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559711 AgrOrtholog
BioCyc Gene G2FUF-2948 BioCyc
Ensembl Genes ENSRNOG00000005303 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007130 ENTREZGENE
  ENSRNOT00000007130.7 UniProtKB/TrEMBL
  ENSRNOT00000099656.1 UniProtKB/TrEMBL
Gene3D-CATH putative rabgap domain of human tbc1 domain family member 14 like domains UniProtKB/TrEMBL
  Ypt/Rab-GAP domain of gyp1p, domain 3 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7097051 IMAGE-MGC_LOAD
InterPro Rab-GTPase_TBC_sf UniProtKB/TrEMBL
  RabGAP_TBC UniProtKB/TrEMBL
KEGG Report rno:302552 UniProtKB/TrEMBL
MGC_CLONE MGC:187398 IMAGE-MGC_LOAD
NCBI Gene 302552 ENTREZGENE
PANTHER TBC1 DOMAIN FAMILY MEMBER 25 UniProtKB/TrEMBL
  TBC1 DOMAIN FAMILY MEMBER GTPASE-ACTIVATING PROTEIN UniProtKB/TrEMBL
Pfam TBC UniProtKB/TrEMBL
PhenoGen Tbc1d25 PhenoGen
PROSITE TBC_RABGAP UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005303 RatGTEx
SMART TBC UniProtKB/TrEMBL
Superfamily-SCOP RabGAP_TBC UniProtKB/TrEMBL
UniProt A0A8I6ALA8 ENTREZGENE, UniProtKB/TrEMBL
  B1WBS1 ENTREZGENE, UniProtKB/TrEMBL
  F7F8Z1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Tbc1d25  TBC1 domain family, member 25   Tbc1d25_predicted  TBC1 domain family, member 25 (predicted)  'predicted' is removed 2292626 APPROVED
2007-01-30 Tbc1d25_predicted  TBC1 domain family, member 25 (predicted)  Oatl1_predicted  ornithine aminotransferase-like 1 (predicted)  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2006-03-30 Oatl1_predicted  ornithine aminotransferase-like 1 (predicted)  RGD1559711_predicted  similar to ornithine aminotransferase-like 1 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1559711_predicted  similar to ornithine aminotransferase-like 1 (predicted)  LOC302552  similar to ornithine aminotransferase-like 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302552  similar to ornithine aminotransferase-like 1      Symbol and Name status set to provisional 70820 PROVISIONAL