Tbc1d23 TBC1 domain family, member 23 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tbc1d23provided by RGD
Official Full Name: TBC1 domain family, member 23provided by RGD
Primary source: RGD:1307925
See related: Ensembl:ENSRNOG00000001642 AllianceGenome:RGD:1307925
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: RGD1307925
Summary: Predicted to be involved in several processes, including embryonic brain development; nervous system development; and vesicle tethering to Golgi. Predicted to act upstream of or within positive regulation of interleukin-6 production; regulation of inflammatory response; and regulation of tumor necrosis factor production. Predicted to be located in Golgi apparatus and cytoplasmic vesicle. Predicted to be part of WASH complex. Predicted to be active in trans-Golgi network. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia. Orthologous to human TBC1D23 (TBC1 domain family member 23). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 168.7), Spleen (RPKM 155.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 11q12

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	11	NC_086029.1 (56772476..56830625)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	11	NC_051346.1 (43303355..43361507)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	11	NC_005110.4 (45401396..45459841)

Chromosome 11 - NC_086029.1 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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Markers

AU015720 (e-PCR)
- UniSTS:209227

RH144429 (e-PCR)
- UniSTS:233674

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in brain development	ISO Inferred from Sequence Orthology more info
involved_in embryonic brain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in embryonic brain development	ISO Inferred from Sequence Orthology more info
involved_in neuron projection development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of interleukin-6 production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde transport, endosome to Golgi	ISO Inferred from Sequence Orthology more info
involved_in vesicle tethering to Golgi	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle tethering to Golgi	ISO Inferred from Sequence Orthology more info
involved_in vesicle-mediated transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
part_of WASH complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
is_active_in trans-Golgi network	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: TBC1 domain family member 23

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_001371895.1 → NP_001358824.1 TBC1 domain family member 23 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

BG673671, JAXUCZ010000011

UniProtKB/TrEMBL

A0A8I5YBN9, D4AAH9

Related

ENSRNOP00000002240.6, ENSRNOT00000002240.8

Conserved Domains (2) summary

pfam00566
Location:48 → 246

RabGAP-TBC; Rab-GTPase-TBC domain

pfam00581
Location:334 → 381

Rhodanese; Rhodanese-like domain
NM_001371896.1 → NP_001358825.1 TBC1 domain family member 23 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

BG673671, JAXUCZ010000011

UniProtKB/TrEMBL

A0A8I5YBN9, A0A8I6AAK0, A6IQM8

Related

ENSRNOP00000089797.1, ENSRNOT00000102661.1

Conserved Domains (2) summary

pfam00566
Location:48 → 246

RabGAP-TBC; Rab-GTPase-TBC domain

pfam00581
Location:334 → 381

Rhodanese; Rhodanese-like domain

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_086029.1 Reference GRCr8

Range

56772476..56830625

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039088379.2 → XP_038944307.1 TBC1 domain family member 23 isoform X1

UniProtKB/TrEMBL

A0A8I5YBN9

Conserved Domains (3) summary

cl02495
Location:4 → 94

RabGAP-TBC; Rab-GTPase-TBC domain

pfam00581
Location:182 → 229

Rhodanese; Rhodanese-like domain

cd20788
Location:427 → 541

TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins
XM_039088380.2 → XP_038944308.1 TBC1 domain family member 23 isoform X2

UniProtKB/TrEMBL

A6IQM9

Conserved Domains (2) summary

pfam00581
Location:101 → 148

Rhodanese; Rhodanese-like domain

cd20788
Location:346 → 460

TBC1D23_C-like; C-terminal domain of TBC1 domain family member 23, and similar proteins

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001107099.1: Suppressed sequence

Description

NM_001107099.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: TBC1D23 (GeneID:55773).