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

Gene ID: 155812, updated on 12-Aug-2018

Summary

Official Symbol
Trim9provided by RGD
Official Full Name
tripartite motif-containing 9provided by RGD
Primary source
RGD:621540
See related
Ensembl:ENSRNOG00000007031
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
RING finger protein; may mediate synaptic vesicle exocytosis by controlling the availability of SNAP-25 [RGD, Feb 2006]
Expression
Biased expression in Brain (RPKM 153.4) and Thymus (RPKM 12.2) See more
Orthologs

Genomic context

See Trim9 in Genome Data Viewer
Location:
6q24
Exon count:
14
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (92660026..92760036, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 6 NC_005105.3 (102107774..102207427, complement)

Chromosome 6 - NC_005105.4Genomic Context describing neighboring genes Neighboring gene abhydrolase domain containing 12B Neighboring gene glycogen phosphorylase L Neighboring gene uncharacterized LOC102549102 Neighboring gene uncharacterized LOC102548972

Genomic regions, transcripts, and products

Expression

  • Project title: 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
SNARE binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
protein domain specific binding ISO
Inferred from Sequence Orthology
more info
 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
 
ubiquitin-protein transferase activity ISO
Inferred from Sequence Orthology
more info
 
ubiquitin-protein transferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
negative regulation of SNARE complex assembly IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of calcium ion-dependent exocytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
 
proteasome-mediated ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
protein ubiquitination IEA
Inferred from Electronic Annotation
more info
 
synaptic vesicle exocytosis IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
cytosol ISO
Inferred from Sequence Orthology
more info
 
dendrite ISO
Inferred from Sequence Orthology
more info
 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
presynaptic cytosol IDA
Inferred from Direct Assay
more info
PubMed 
synaptic vesicle EXP
Inferred from Experiment
more info
PubMed 
synaptic vesicle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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
XP_008762913.1
XP_008762914.1
XP_008762915.1
XP_008762916.1
XP_017449485.1
XP_017449486.1
XP_017449487.1
XP_017449488.1
XP_017449489.1
XP_017449490.1
XP_017449491.1
XP_017449493.1
XP_017449494.1
XP_017449495.1
XP_017449496.1

NCBI Reference Sequences (RefSeq)

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)

  1. NM_130420.1NP_569104.1  E3 ubiquitin-protein ligase TRIM9

    See identical proteins and their annotated locations for NP_569104.1

    Status: PROVISIONAL

    Source sequence(s)
    AF350422
    UniProtKB/Swiss-Prot
    Q91ZY8
    Related
    ENSRNOP00000009559.1, ENSRNOT00000009560.2
    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:453532
    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:529700
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
    cd16755
    Location:552
    RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005105.4 Reference Rnor_6.0 Primary Assembly

    Range
    92660026..92760036 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017593998.1XP_017449487.1  E3 ubiquitin-protein ligase TRIM9 isoform X4

  2. XM_017593999.1XP_017449488.1  E3 ubiquitin-protein ligase TRIM9 isoform X5

    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:453532
    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 ...
    cd00162
    Location:938
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cd12889
    Location:620785
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
  3. XM_008764693.2XP_008762915.1  E3 ubiquitin-protein ligase TRIM9 isoform X7

    See identical proteins and their annotated locations for XP_008762915.1

    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:453532
    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:630777
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
    cd16755
    Location:552
    RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
  4. XM_017593996.1XP_017449485.1  E3 ubiquitin-protein ligase TRIM9 isoform X2

    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:453532
    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 ...
    cd00162
    Location:938
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cd12889
    Location:630795
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
  5. XM_008764692.2XP_008762914.1  E3 ubiquitin-protein ligase TRIM9 isoform X6

    See identical proteins and their annotated locations for XP_008762914.1

    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:453532
    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:631778
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
    cd16755
    Location:552
    RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
  6. XM_017593997.1XP_017449486.1  E3 ubiquitin-protein ligase TRIM9 isoform X3

  7. XM_008764691.2XP_008762913.1  E3 ubiquitin-protein ligase TRIM9 isoform X1

    See identical proteins and their annotated locations for XP_008762913.1

    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:453532
    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:631796
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
    cd16755
    Location:552
    RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
  8. XM_008764694.2XP_008762916.1  E3 ubiquitin-protein ligase TRIM9 isoform X15

    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:449528
    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 ...
    cd00162
    Location:938
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cd12889
    Location:525696
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
  9. XM_017594006.1XP_017449495.1  E3 ubiquitin-protein ligase TRIM9 isoform X13

  10. XM_017594007.1XP_017449496.1  E3 ubiquitin-protein ligase TRIM9 isoform X14

    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:453532
    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:557704
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
    cd16755
    Location:552
    RING-HC_TRIM9; RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins
  11. XM_017594002.1XP_017449491.1  E3 ubiquitin-protein ligase TRIM9 isoform X10

    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:453532
    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 ...
    cd00162
    Location:938
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cd12889
    Location:557722
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
  12. XM_017594005.1XP_017449494.1  E3 ubiquitin-protein ligase TRIM9 isoform X12

  13. XM_017594001.1XP_017449490.1  E3 ubiquitin-protein ligase TRIM9 isoform X9

    Conserved Domains (5) summary
    smart00502
    Location:273399
    BBC; B-Box C-terminal domain
    smart00336
    Location:224266
    BBOX; B-Box-type zinc finger
    cd00063
    Location:453532
    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 ...
    cd00162
    Location:938
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cd12889
    Location:567732
    SPRY_PRY_TRIM67_9; PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67
  14. XM_017594004.1XP_017449493.1  E3 ubiquitin-protein ligase TRIM9 isoform X11

  15. XM_017594000.1XP_017449489.1  E3 ubiquitin-protein ligase TRIM9 isoform X8

Alternate Rn_Celera

Genomic

  1. AC_000074.1 Alternate Rn_Celera

    Range
    87245397..87344755 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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