Trim40 (tripartite motif-containing 40) - Rat Genome Database

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Gene: Trim40 (tripartite motif-containing 40) Rattus norvegicus
Analyze
Symbol: Trim40
Name: tripartite motif-containing 40
RGD ID: 1359645
Description: Predicted to enable ubiquitin protein ligase activity. Involved in negative regulation of NF-kappaB transcription factor activity and negative regulation of cell growth. Predicted to be part of IkappaB kinase complex. Predicted to be active in cytoplasm. Orthologous to human TRIM40 (tripartite motif containing 40); INTERACTS WITH bisphenol A; linsidomine; 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: E3 ubiquitin ligase TRIM40; probable E3 NEDD8-protein ligase; RING finger protein 35; Rnf35; tripartite motif protein 40; tripartite motif-containing protein 40; tripartite motif-containing protein 40-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8201,680,554 - 1,691,123 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl201,681,333 - 1,691,123 (+)EnsemblGRCr8
mRatBN7.2201,676,114 - 1,685,906 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl201,676,270 - 1,685,214 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx201,729,830 - 1,738,396 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0201,733,332 - 1,741,894 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0201,673,911 - 1,682,490 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0202,169,674 - 2,178,477 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl202,169,545 - 2,178,601 (+)Ensemblrn6Rnor6.0
Rnor_5.0204,205,817 - 4,216,051 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4201,768,482 - 1,777,393 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera202,385,041 - 2,394,038 (+)NCBICelera
RGSC_v3.1201,768,481 - 1,777,393 (+)NCBI
Cytogenetic Map20p12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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

Cellular Component

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. TRIM40 promotes neddylation of IKKgamma and is downregulated in gastrointestinal cancers. Noguchi K, etal., Carcinogenesis. 2011 Jul;32(7):995-1004. doi: 10.1093/carcin/bgr068. Epub 2011 Apr 7.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15060004  


Genomics

Comparative Map Data
Trim40
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8201,680,554 - 1,691,123 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl201,681,333 - 1,691,123 (+)EnsemblGRCr8
mRatBN7.2201,676,114 - 1,685,906 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl201,676,270 - 1,685,214 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx201,729,830 - 1,738,396 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0201,733,332 - 1,741,894 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0201,673,911 - 1,682,490 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0202,169,674 - 2,178,477 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl202,169,545 - 2,178,601 (+)Ensemblrn6Rnor6.0
Rnor_5.0204,205,817 - 4,216,051 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4201,768,482 - 1,777,393 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera202,385,041 - 2,394,038 (+)NCBICelera
RGSC_v3.1201,768,481 - 1,777,393 (+)NCBI
Cytogenetic Map20p12NCBI
TRIM40
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38630,136,140 - 30,148,735 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl630,136,028 - 30,151,592 (+)Ensemblhg38GRCh38
GRCh37630,103,917 - 30,116,512 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36630,212,489 - 30,224,488 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34630,212,488 - 30,223,570NCBI
Celera631,702,776 - 31,714,781 (+)NCBICelera
Cytogenetic Map6p22.1NCBI
HuRef629,902,691 - 29,914,687 (+)NCBIHuRef
CHM1_1630,106,586 - 30,118,587 (+)NCBICHM1_1
T2T-CHM13v2.0630,000,415 - 30,013,010 (+)NCBIT2T-CHM13v2.0
Trim40
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391737,192,488 - 37,201,049 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1737,192,490 - 37,201,015 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381736,881,596 - 36,890,157 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1736,881,598 - 36,890,123 (-)Ensemblmm10GRCm38
MGSCv371737,018,543 - 37,027,070 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361736,489,651 - 36,498,098 (-)NCBIMGSCv36mm8
Celera1740,300,820 - 40,309,325 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1719.16NCBI
Trim40
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955583242,054 - 259,008 (+)Ensembl
ChiLan1.0NW_004955583242,054 - 260,565 (+)NCBIChiLan1.0ChiLan1.0
TRIM40
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2544,720,791 - 44,744,925 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1640,683,795 - 40,704,421 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0629,912,857 - 29,926,550 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1630,583,968 - 30,596,583 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl630,584,272 - 30,599,635 (+)EnsemblpanPan2panpan1.1
Trim40
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494632,681,400 - 32,696,823 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936723896,054 - 909,263 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936723897,213 - 909,263 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRIM40
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl722,702,925 - 22,717,511 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1722,702,891 - 22,717,850 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2724,860,690 - 24,873,040 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRIM40
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11742,358,748 - 42,370,400 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604429,786,939 - 29,798,392 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Trim40
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475425,278,747 - 25,285,378 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Trim40
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1189,852,521 - 9,862,235 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Trim40
107 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:108
Count of miRNA genes:91
Interacting mature miRNAs:94
Transcripts:ENSRNOT00000029070
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015332005306452Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2016693431Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)2016693431Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013629303Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

Markers in Region
D20Yum3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2201,679,261 - 1,679,465 (+)MAPPERmRatBN7.2
Rnor_6.0202,172,537 - 2,172,740NCBIRnor6.0
Rnor_5.0204,209,526 - 4,209,729UniSTSRnor5.0
RGSC_v3.4201,771,345 - 1,771,548UniSTSRGSC3.4
Celera202,387,904 - 2,388,107UniSTS
Cytogenetic Map20p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
16 1 3 17 16 11 7 11 37 9 2 1 24 5

Sequence


Ensembl Acc Id: ENSRNOT00000029070   ⟹   ENSRNOP00000035419
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl201,676,270 - 1,685,214 (+)Ensembl
Rnor_6.0 Ensembl202,169,545 - 2,178,601 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000120475   ⟹   ENSRNOP00000098139
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl201,681,333 - 1,691,123 (+)Ensembl
RefSeq Acc Id: NM_001009175   ⟹   NP_001009175
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8201,681,333 - 1,691,123 (+)NCBI
mRatBN7.2201,676,114 - 1,685,906 (+)NCBI
Rnor_6.0202,169,674 - 2,178,469 (+)NCBI
Rnor_5.0204,205,817 - 4,216,051 (+)NCBI
RGSC_v3.4201,768,482 - 1,777,393 (+)RGD
Celera202,385,041 - 2,394,038 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063279326   ⟹   XP_063135396
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8201,680,554 - 1,691,123 (+)NCBI
RefSeq Acc Id: XM_063279327   ⟹   XP_063135397
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8201,680,554 - 1,691,123 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001009175 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135396 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135397 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAE84059 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000035419.5
  ENSRNOP00000098139
GenBank Protein Q6MFY8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001009175   ⟸   NM_001009175
- UniProtKB: Q6MFY8 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000035419   ⟸   ENSRNOT00000029070
RefSeq Acc Id: XP_063135396   ⟸   XM_063279326
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063135397   ⟸   XM_063279327
- Peptide Label: isoform X2
- UniProtKB: Q6MFY8 (UniProtKB/Swiss-Prot)
Ensembl Acc Id: ENSRNOP00000098139   ⟸   ENSRNOT00000120475

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MFY8-F1-model_v2 AlphaFold Q6MFY8 1-247 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:1359645 AgrOrtholog
BioCyc Gene G2FUF-4973 BioCyc
Ensembl Genes ENSRNOG00000000783 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000029070.7 UniProtKB/Swiss-Prot
  ENSRNOT00000120475 ENTREZGENE
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot
  Classic Zinc Finger UniProtKB/Swiss-Prot
InterPro TRIM/RBCC UniProtKB/Swiss-Prot
  Znf_B-box UniProtKB/Swiss-Prot
  Znf_C3HC4_RING-type UniProtKB/Swiss-Prot
  Znf_RING UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
  Znf_RING_CS UniProtKB/Swiss-Prot
KEGG Report rno:365528 UniProtKB/Swiss-Prot
NCBI Gene 365528 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE TRIM UniProtKB/Swiss-Prot
Pfam zf-C3HC4 UniProtKB/Swiss-Prot
PhenoGen Trim40 PhenoGen
PROSITE ZF_BBOX UniProtKB/Swiss-Prot
  ZF_RING_1 UniProtKB/Swiss-Prot
  ZF_RING_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000000783 RatGTEx
SMART RING UniProtKB/Swiss-Prot
Superfamily-SCOP B-box zinc-binding domain UniProtKB/Swiss-Prot
  RING/U-box UniProtKB/Swiss-Prot
UniProt Q6MFY8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Trim40  tripartite motif-containing 40  LOC100364386  tripartite motif-containing protein 40-like  Data merged from RGD:2321173 1643240 APPROVED
2010-05-05 LOC100364386  tripartite motif-containing protein 40-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-07 Trim40  tripartite motif-containing 40  Trim40  tripartite motif protein 40  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Trim40  tripartite motif protein 40    tripartite motif-containing 40  Name updated 1299863 APPROVED
2005-12-06 Trim40  tripartite motif-containing 40      Symbol and Name updated 1559027 APPROVED
2005-11-17 Trim40  tripartite motif-containing 40      Symbol and Name status set to approved 1299863 APPROVED
2005-07-29 Trim40  tripartite motif-containing 40      Symbol and Name status set to provisional 70820 PROVISIONAL