Ube3d ubiquitin protein ligase E3D [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ube3dprovided by RGD
Official Full Name: ubiquitin protein ligase E3Dprovided by RGD
Primary source: RGD:1306773
See related: EnsemblRapid:ENSRNOG00000010802 AllianceGenome:RGD:1306773
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
Also known as: Ube2cbp; RGD1306773
Summary: Predicted to enable cyclin binding activity; ubiquitin conjugating enzyme binding activity; and ubiquitin protein ligase activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process and protein ubiquitination. Predicted to be located in membrane. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytosol and nucleus. Orthologous to human UBE3D (ubiquitin protein ligase E3D). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 23.7), Kidney (RPKM 21.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q31

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (96125609..96293122, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (87245503..87413104, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (93948689..94120477, complement)

Chromosome 8 - NC_086026.1 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
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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables cyclin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cyclin binding	IEA Inferred from Electronic Annotation more info
enables cyclin binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin conjugating enzyme binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-like protein conjugating enzyme binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin-like protein conjugating enzyme binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein autoubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein autoubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein autoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein monoubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein monoubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein monoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein polyubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein polyubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein polyubiquitination	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytosol	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of ubiquitin ligase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ubiquitin ligase complex	IEA Inferred from Electronic Annotation more info
part_of ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase E3D

Names: HECT-type E3 ubiquitin transferase E3D; UbcH10 binding protein with a hect-like domain; ubcH10-binding protein with a HECT-like domain; ubiquitin-conjugating enzyme E2C-binding protein

NP_001034699.1

EC 2.3.2.26

XP_006243541.1

EC 2.3.2.26

XP_038937459.1

EC 2.3.2.26

XP_038937460.1

EC 2.3.2.26

XP_063121630.1

EC 2.3.2.26

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_001039610.2 → NP_001034699.1 E3 ubiquitin-protein ligase E3D isoform 1

See identical proteins and their annotated locations for NP_001034699.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/Swiss-Prot

Q3T1H6

UniProtKB/TrEMBL

A0A0G2JZS6

Related

ENSRNOP00000014600.4, ENSRNOT00000014600.7

Conserved Domains (1) summary

pfam09814
Location:13 → 358

HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
NM_001433776.1 → NP_001420705.1 E3 ubiquitin-protein ligase E3D isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008
NM_001433777.1 → NP_001420706.1 E3 ubiquitin-protein ligase E3D isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008
NM_001433778.1 → NP_001420707.1 E3 ubiquitin-protein ligase E3D isoform 4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

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_086026.1 Reference GRCr8

Range

96125609..96293122 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063265560.1 → XP_063121630.1 E3 ubiquitin-protein ligase E3D isoform X2
XM_006243479.5 → XP_006243541.1 E3 ubiquitin-protein ligase E3D isoform X1

UniProtKB/TrEMBL

A0A0G2JZS6

Related

ENSRNOP00000110873.1, ENSRNOT00000134165.1

Conserved Domains (1) summary

pfam09814
Location:13 → 358

HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
XM_039081532.2 → XP_038937460.1 E3 ubiquitin-protein ligase E3D isoform X3

UniProtKB/TrEMBL

A6I1U0

Conserved Domains (1) summary

cl19900
Location:73 → 179

HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding
XM_039081531.2 → XP_038937459.1 E3 ubiquitin-protein ligase E3D isoform X3

UniProtKB/TrEMBL

A6I1U0

Conserved Domains (1) summary

cl19900
Location:73 → 179

HECT_2; HECT-like Ubiquitin-conjugating enzyme (E2)-binding