Trim9 tripartite motif-containing 9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Trim9provided by RGD
Official Full Name: tripartite motif-containing 9provided by RGD
Primary source: RGD:621540
See related: EnsemblRapid:ENSRNOG00000007031 AllianceGenome:RGD:621540
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables SNARE binding activity. Involved in negative regulation of SNARE complex assembly; negative regulation of calcium ion-dependent exocytosis; and synaptic vesicle exocytosis. Is active in presynaptic cytosol and synaptic vesicle. Orthologous to human TRIM9 (tripartite motif containing 9). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in Brain (RPKM 153.4) and Thymus (RPKM 12.2) See more
Orthologs: human mouse all
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Genomic context

Location:: 6q24

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (94492789..94592597, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (88756824..88856588, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (92660026..92760036, complement)

Chromosome 6 - NC_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Trim9 regulates the directional differentiation of retinal Muller cells to retinal ganglion cells.
Title: Trim9 regulates the directional differentiation of retinal Müller cells to retinal ganglion cells.
TRIM9 promotes Muller cell-derived retinal stem cells to differentiate into retinal ganglion cells by regulating Atoh7.
Title: TRIM9 promotes Müller cell-derived retinal stem cells to differentiate into retinal ganglion cells by regulating Atoh7.
Knockdown of TRIM9 attenuates irinotecaninduced intestinal mucositis in IEC6 cells by regulating DUSP6 expression via the P38 pathway.
Title: Knockdown of TRIM9 attenuates irinotecan‑induced intestinal mucositis in IEC‑6 cells by regulating DUSP6 expression via the P38 pathway.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Trim9 (e-PCR), detects polymorphism
- UniSTS:507889

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables SNARE binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in negative regulation of SNARE complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of calcium ion-dependent exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle exocytosis	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
is_active_in presynaptic cytosol	IDA Inferred from Direct Assay more info	PubMed
is_active_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed
is_active_in synaptic vesicle	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: E3 ubiquitin-protein ligase TRIM9

Names: RING-type E3 ubiquitin transferase TRIM9; SNAP-25-interacting RING finger protein; Spring; tripartite motif protein 9; tripartite motif-containing protein 9

NP_569104.1

EC 2.3.2.27

XP_008762913.1

EC 2.3.2.27

XP_008762914.1

EC 2.3.2.27

XP_008762915.1

EC 2.3.2.27

XP_008762916.1

EC 2.3.2.27

XP_017449485.1

EC 2.3.2.27

XP_017449487.1

EC 2.3.2.27

XP_017449488.1

EC 2.3.2.27

XP_038967632.1

EC 2.3.2.27

XP_038967633.1

EC 2.3.2.27

XP_038967634.1

EC 2.3.2.27

XP_063117563.1

EC 2.3.2.27

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001434144.1 → NP_001421073.1 E3 ubiquitin-protein ligase TRIM9 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006
NM_001434145.1 → NP_001421074.1 E3 ubiquitin-protein ligase TRIM9 isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006
NM_001434146.1 → NP_001421075.1 E3 ubiquitin-protein ligase TRIM9 isoform 4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006
NM_001434147.1 → NP_001421076.1 E3 ubiquitin-protein ligase TRIM9 isoform 5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006
NM_001434148.1 → NP_001421077.1 E3 ubiquitin-protein ligase TRIM9 isoform 6

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006
NM_001434149.1 → NP_001421078.1 E3 ubiquitin-protein ligase TRIM9 isoform 7

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006
NM_001434150.1 → NP_001421079.1 E3 ubiquitin-protein ligase TRIM9 isoform 8

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006
NM_130420.2 → NP_569104.1 E3 ubiquitin-protein ligase TRIM9 isoform 1

See identical proteins and their annotated locations for NP_569104.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/Swiss-Prot

Q91ZY8

UniProtKB/TrEMBL

A0A8I5ZL10, A6HBZ2

Related

ENSRNOP00000009559.1, ENSRNOT00000009560.4

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:453 → 532

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:529 → 700

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086024.1 Reference GRCr8

Range

94492789..94592597 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039111706.2 → XP_038967634.1 E3 ubiquitin-protein ligase TRIM9 isoform X10

UniProtKB/TrEMBL

A0A8I5XWL7

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:453 → 532

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:529 → 682

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
XM_039111705.2 → XP_038967633.1 E3 ubiquitin-protein ligase TRIM9 isoform X8

UniProtKB/TrEMBL

A0A8I5XWL7

Related

ENSRNOP00000086601.1, ENSRNOT00000112240.2

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:453 → 532

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:620 → 767

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
XM_017593999.3 → XP_017449488.1 E3 ubiquitin-protein ligase TRIM9 isoform X4

UniProtKB/TrEMBL

A0A8I5ZL10

Related

ENSRNOP00000077889.2, ENSRNOT00000094403.2

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:453 → 532

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:620 → 785

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
XM_008764693.4 → XP_008762915.1 E3 ubiquitin-protein ligase TRIM9 isoform X7

UniProtKB/TrEMBL

A0A8I5XWL7

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:453 → 532

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:630 → 777

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
XM_017593996.3 → XP_017449485.1 E3 ubiquitin-protein ligase TRIM9 isoform X2

UniProtKB/TrEMBL

A0A8I5ZL10

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:453 → 532

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:630 → 795

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
XM_008764692.4 → XP_008762914.1 E3 ubiquitin-protein ligase TRIM9 isoform X6

UniProtKB/TrEMBL

A0A8I5XWL7

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:453 → 532

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:631 → 778

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
XM_008764691.3 → XP_008762913.1 E3 ubiquitin-protein ligase TRIM9 isoform X1

UniProtKB/TrEMBL

A0A8I5ZL10, A0A8I6AAA7

Related

ENSRNOP00000088626.1, ENSRNOT00000106074.2

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:453 → 532

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:631 → 796

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
XM_063261493.1 → XP_063117563.1 E3 ubiquitin-protein ligase TRIM9 isoform X11
XM_008764694.4 → XP_008762916.1 E3 ubiquitin-protein ligase TRIM9 isoform X9

UniProtKB/TrEMBL

A0A8I5ZL10

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:449 → 528

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:525 → 696

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
XM_039111704.2 → XP_038967632.1 E3 ubiquitin-protein ligase TRIM9 isoform X5

UniProtKB/TrEMBL

A0A8I5ZL10

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:449 → 528

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:616 → 781

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
XM_017593998.3 → XP_017449487.1 E3 ubiquitin-protein ligase TRIM9 isoform X3

UniProtKB/TrEMBL

A0A8I5ZL10

Conserved Domains (6) summary

smart00502
Location:273 → 399

BBC; B-Box C-terminal domain

cd00063
Location:449 → 528

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12889
Location:627 → 792

SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67

cd16755
Location:5 → 52

RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19826
Location:223 → 271

Bbox2_TRIM9_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

cd19843
Location:166 → 212

Bbox1_TRIM9_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins