Trim13 (tripartite motif containing 13)

Gene: Trim13 (tripartite motif containing 13) Ictidomys tridecemlineatus

Analyze

Symbol:

Trim13

Name:

tripartite motif containing 13

RGD ID:

12649307

Description:

ENCODES a protein that exhibits metal ion binding (inferred); transcription coactivator activity (inferred); ubiquitin protein ligase activity (inferred); INVOLVED IN ERAD pathway (inferred); innate immune response (inferred); negative regulation of viral transcription (inferred); ASSOCIATED WITH chromosome 13q14 deletion syndrome (ortholog); genetic disease (ortholog); intellectual disability (ortholog); FOUND IN cytoplasm (inferred); endoplasmic reticulum (inferred); endoplasmic reticulum membrane (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

E3 ubiquitin-protein ligase TRIM13; tripartite motif containing 13, transcript variant X1; tripartite motif containing 13, transcript variant X2

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	159,466,050 - 159,505,345 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936565	2,976,729 - 2,989,088 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936565	2,976,681 - 2,989,036 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

chromosome 13q14 deletion syndrome (ISO)

genetic disease (ISO)

intellectual disability (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

ERAD pathway (IEA)

innate immune response (IEA)

negative regulation of viral transcription (IEA)

positive regulation of canonical NF-kappaB signal transduction (IEA)

positive regulation of DNA-templated transcription (IEA)

positive regulation of macroautophagy (IEA)

proteasome-mediated ubiquitin-dependent protein catabolic process (IEA)

protein autoubiquitination (IEA)

protein ubiquitination (IEA)

suppression of viral release by host (IEA)

Cellular Component

cytoplasm (IEA)

endoplasmic reticulum (IEA)

endoplasmic reticulum membrane (IEA)

membrane (IEA)

perinuclear endoplasmic reticulum (IEA)

Molecular Function

metal ion binding (IEA)

protein binding (ISO)

transcription coactivator activity (IEA)

ubiquitin protein ligase activity (IEA)

ubiquitin-like protein ligase activity (IEA)

ubiquitin-protein transferase activity (IEA)

zinc ion binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Trim13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	159,466,050 - 159,505,345 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936565	2,976,729 - 2,989,088 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936565	2,976,681 - 2,989,036 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TRIM13
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	13	49,997,042 - 50,018,467 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	13	49,995,888 - 50,020,481 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	13	50,571,178 - 50,592,603 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	13	49,469,144 - 49,490,604 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	13	49,469,143 - 49,490,604	NCBI
Celera	13	31,625,838 - 31,647,244 (+)	NCBI		Celera
Cytogenetic Map	13	q14.2	NCBI
HuRef	13	31,366,258 - 31,387,677 (+)	NCBI		HuRef
CHM1_1	13	50,539,021 - 50,560,434 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	13	49,217,709 - 49,239,060 (+)	NCBI		T2T-CHM13v2.0

Trim13
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	14	61,835,675 - 61,847,736 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	14	61,835,696 - 61,843,395 (+)	Ensembl		GRCm39 Ensembl
GRCm38	14	61,598,226 - 61,610,287 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	14	61,598,247 - 61,605,946 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	14	62,217,063 - 62,224,783 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	14	60,553,904 - 60,560,053 (+)	NCBI		MGSCv36	mm8
Celera	14	59,365,665 - 59,373,386 (+)	NCBI		Celera
Cytogenetic Map	14	D1	NCBI
cM Map	14	33.16	NCBI

Trim13
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	15	39,909,587 - 39,948,719 (+)	NCBI		GRCr8
mRatBN7.2	15	35,733,548 - 35,772,676 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	35,734,107 - 35,772,677 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	15	37,628,710 - 37,637,209 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	15	38,779,334 - 38,787,833 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	15	37,224,529 - 37,233,010 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	15	41,897,191 - 41,936,545 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	41,927,241 - 41,935,718 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	45,698,405 - 45,736,734 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	40,743,520 - 40,752,138 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	15	40,759,219 - 40,767,837 (+)	NCBI
Celera	15	35,459,278 - 35,467,759 (+)	NCBI		Celera
Cytogenetic Map	15	p12	NCBI

Trim13
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955431	3,324,331 - 3,395,724 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955431	3,324,331 - 3,395,724 (+)	NCBI	ChiLan1.0	ChiLan1.0

TRIM13
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	14	51,379,791 - 51,456,362 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	13	50,031,066 - 50,107,604 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	13	31,137,236 - 31,153,398 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	13	49,881,218 - 49,900,496 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	13	49,889,041 - 49,900,488 (+)	Ensembl	panpan1.1		panPan2

TRIM13
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	22	1,877,672 - 1,893,097 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	22	1,871,181 - 1,910,055 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	22	1,906,832 - 1,939,184 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	22	1,867,318 - 1,899,835 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	22	1,860,815 - 1,899,769 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	22	1,777,349 - 1,809,693 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	22	1,826,477 - 1,858,961 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	22	1,844,955 - 1,877,312 (-)	NCBI		UU_Cfam_GSD_1.0

TRIM13
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	11	17,793,784 - 17,849,732 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	11	17,785,031 - 17,850,005 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	11	18,183,419 - 18,187,816 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TRIM13
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	3	27,851,552 - 27,925,379 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	3	27,924,150 - 27,925,373 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666057	15,944,809 - 16,032,693 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Trim13
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624748	4,683,518 - 4,765,944 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005330210	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_013360727	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040281550	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040281551	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040281552	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040281553	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSTOT00000021439 ⟹ ENSSTOP00000016425

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936565	2,976,729 - 2,989,088 (+)	Ensembl

RefSeq Acc Id:

XM_005330210 ⟹ XP_005330267

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404945	159,492,642 - 159,505,345 (+)	NCBI
SpeTri2.0	NW_004936565	2,976,681 - 2,989,036 (+)	NCBI

Sequence:

show sequence

AGGTACACGCCGGGGGTGGAGTCCGAGGTGCCAACGGAGGAGGGCGGGGCCTGTGCAGCGCCTC
GAGTCCATTTTGCGGCGGTGCGAGGCTCTTACCGCGTGATCTTCCGAGCTGGAAGACCCGAGGC
CTTGCAGCTGCAGGCTTTGCCGGAGGATGTGATGGAGCTGCTTGAAGAAGATCTCACGTGTCCA
ATTTGTTGCAGTCTGTTTGATGATCCTCGAGTTTTGCCTTGTTCACACAACTTCTGCAAAAAAT
GCTTAGAAGGTCTCTTAGAGGGGAATGTGCGGAATTCGTTGTGGAGACCATCTCCATTCAAGTG
CCCTACATGCCGGAAGGAAACCTCAGCTACTGGAGTTAATAGCCTGCAGGTTAATTACTCCCTG
AAAGGTATTGTGGAGAAATACAACAAAATCAAGGTCTCTCCCAAAATGCCAGTGTGCAAAGGAC
ACTTGGGGCAGCCTCTAAACATTTTCTGCCTAACTGATATGCAGCTAATTTGTGGGATCTGTGC
TACTCGAGGTGACCACACCAAGCATGTCTTCTGTTCTATTGAAGATGCCTATGCTCAGGAAAGG
GATGCCTTTGAGACTCTCTTCCAGAGTTTTGAGACCTGGCGTCGGGGAGATGCTCTTTCTCGTT
TGGATACCTTGGAAACCAGTAAGAGGAAATCCCTGCAGTTACTAACTAAAGATTCAGATAAAGT
GAAGGAATTTTTTGAGAAGTTACAACACACATTGGATCAAAAGAAGAATGAAATCCTGTCTGAC
TTTGAGACCATGAAACTTGCAGTAATGCAAGCTTATGACCCAGAGATCAACAAACTCAATACCA
TCTTGCAGGAGCAACGAATGGCTTTTAATATTGCTGAGGCTTTCAAAGATGTGTCAGAACCCAT
TGTATTTCTGCAACAGATGCAGGAGTTCAGGGAGAAAATCAAAGTAATCAAGGAAACTCCTTTA
CCTCCCTCTACTTTGCCCACAAGCCCTTTAATGAAGAACTTTGATACCAGTCAATGGGAGGACA
TAAAACTAGTAGATGTGGATAAACTTTCTTTGCCTCAAGATACTGGCACGTTCATAAGCAAGAT
TCCTTGGAGATTCTATCAGTTATTTGTGGTACTCCTTCTACTTGGCCTCCTTATTTTCCTCATT
TTCTTGGGTCCTACTGTATTCCTAGAATGGTCTGTATTTGATGAACTGGCAATTTGGAAAGACC
ATCTTTCTAATTTCAGTTTTTATCTGACTAAATCAGCTGATTTTGTAGAACAATCAGTTTTTTA
CTGGGAACAAGTGACAAATGGGTTTTTCATTTTCAGTGAAACAGTCAACAATTTTACTTTGGTG
GTGCTAAATAATGTGGCCGAATTTGTGTGCAAATATAAACTATTATAAAATCTTCCAACTCTGC
A

hide sequence

RefSeq Acc Id:

XM_040281550 ⟹ XP_040137484

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404945	159,466,050 - 159,505,345 (+)	NCBI

RefSeq Acc Id:

XM_040281551 ⟹ XP_040137485

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404945	159,492,673 - 159,505,345 (+)	NCBI

RefSeq Acc Id:

XM_040281552 ⟹ XP_040137486

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404945	159,492,679 - 159,505,345 (+)	NCBI

RefSeq Acc Id:

XM_040281553 ⟹ XP_040137487

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404945	159,494,574 - 159,505,345 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_005330267	(Get FASTA)	NCBI Sequence Viewer
	XP_040137484	(Get FASTA)	NCBI Sequence Viewer
	XP_040137485	(Get FASTA)	NCBI Sequence Viewer
	XP_040137486	(Get FASTA)	NCBI Sequence Viewer
	XP_040137487	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000016425.1
GenBank Protein	KAG3293108	(Get FASTA)	NCBI Sequence Viewer
	KAG3293109	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_005330267 ⟸ XM_005330210

- UniProtKB:

I3MWD0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MELLEEDLTCPICCSLFDDPRVLPCSHNFCKKCLEGLLEGNVRNSLWRPSPFKCPTCRKETSAT
GVNSLQVNYSLKGIVEKYNKIKVSPKMPVCKGHLGQPLNIFCLTDMQLICGICATRGDHTKHVF
CSIEDAYAQERDAFETLFQSFETWRRGDALSRLDTLETSKRKSLQLLTKDSDKVKEFFEKLQHT
LDQKKNEILSDFETMKLAVMQAYDPEINKLNTILQEQRMAFNIAEAFKDVSEPIVFLQQMQEFR
EKIKVIKETPLPPSTLPTSPLMKNFDTSQWEDIKLVDVDKLSLPQDTGTFISKIPWRFYQLFVV
LLLLGLLIFLIFLGPTVFLEWSVFDELAIWKDHLSNFSFYLTKSADFVEQSVFYWEQVTNGFFI
FSETVNNFTLVVLNNVAEFVCKYKLL

hide sequence

RefSeq Acc Id:	XP_040137484 ⟸ XM_040281550
- UniProtKB:	I3MWD0 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_040137485 ⟸ XM_040281551
- UniProtKB:	I3MWD0 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_040137486 ⟸ XM_040281552
- UniProtKB:	I3MWD0 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_040137487 ⟸ XM_040281553
- UniProtKB:	I3MWD0 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSSTOP00000016425 ⟸ ENSSTOT00000021439

Protein Domains

B box-type RING-type

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000024506	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000021439.2	UniProtKB/TrEMBL
Gene3D-CATH	3.30.40.10	UniProtKB/TrEMBL
	Classic Zinc Finger	UniProtKB/TrEMBL
InterPro	Znf-RING_LisH	UniProtKB/TrEMBL
	Znf_B-box	UniProtKB/TrEMBL
	Znf_RING	UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/TrEMBL
	Znf_RING_CS	UniProtKB/TrEMBL
NCBI Gene	Trim13	ENTREZGENE
PANTHER	E3 UBIQUITIN-PROTEIN LIGASE TRIM	UniProtKB/TrEMBL
	E3 UBIQUITIN-PROTEIN LIGASE TRIM13	UniProtKB/TrEMBL
Pfam	zf-B_box	UniProtKB/TrEMBL
	zf-RING_UBOX	UniProtKB/TrEMBL
PROSITE	ZF_BBOX	UniProtKB/TrEMBL
	ZF_RING_1	UniProtKB/TrEMBL
	ZF_RING_2	UniProtKB/TrEMBL
SMART	BBOX	UniProtKB/TrEMBL
	RING	UniProtKB/TrEMBL
Superfamily-SCOP	B-box zinc-binding domain	UniProtKB/TrEMBL
	RING/U-box	UniProtKB/TrEMBL
UniProt	I3MWD0	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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