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TBC1D1 TBC1 domain family member 1 [ Homo sapiens (human) ]

Gene ID: 23216, updated on 20-Mar-2020

Summary

Official Symbol
TBC1D1provided by HGNC
Official Full Name
TBC1 domain family member 1provided by HGNC
Primary source
HGNC:HGNC:11578
See related
Ensembl:ENSG00000065882 MIM:609850
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TBC; TBC1
Summary
TBC1D1 is the founding member of a family of proteins sharing a 180- to 200-amino acid TBC domain presumed to have a role in regulating cell growth and differentiation. These proteins share significant homology with TRE2 (USP6; MIM 604334), yeast Bub2, and CDC16 (MIM 603461) (White et al., 2000 [PubMed 10965142]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in endometrium (RPKM 22.4), kidney (RPKM 18.2) and 24 other tissues See more
Orthologs

Genomic context

See TBC1D1 in Genome Data Viewer
Location:
4p14
Exon count:
31
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (37891084..38139175)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (37889606..38140796)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene phosphoglucomutase 2 Neighboring gene heterogeneous nuclear ribonucleoprotein R pseudogene 3 Neighboring gene uncharacterized LOC105374407 Neighboring gene pituitary tumor-transforming 2 Neighboring gene proteasome activator subunit 2 pseudogene 4 Neighboring gene mitochondrial ribosomal protein S33 pseudogene 2 Neighboring gene skeletal muscle cis-regulatory module in TBC1D1 intron Neighboring gene uncharacterized LOC105374408 Neighboring gene uncharacterized LOC105374409

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
NHGRI GWA Catalog
Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations.
NHGRI GWA Catalog
Genome-wide association study of periodontal pathogen colonization.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1108

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Rab GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
activation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane organization TAS
Traceable Author Statement
more info
 
NOT regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein localization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
TBC1 domain family member 1
Names
TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 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_001253912.2NP_001240841.1  TBC1 domain family member 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has multiple differences in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK074954, AK295746, AW364769, BC050321, BQ672157, CR996632, DB036208
    Consensus CDS
    CCDS58897.1
    UniProtKB/Swiss-Prot
    Q86TI0
    UniProtKB/TrEMBL
    Q8NC59
    Related
    ENSP00000423651.1, ENST00000508802.5
    Conserved Domains (5) summary
    smart00164
    Location:8911028
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164371
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:543838
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:789839
    DUF3350; Domain of unknown function (DUF3350)
  2. NM_001253913.1NP_001240842.1  TBC1 domain family member 1 isoform 3

    See identical proteins and their annotated locations for NP_001240842.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a large portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which has a significantly shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC098680, AC108933, AK057182, AK074954, AW364769
    UniProtKB/TrEMBL
    Q8NC59
    Conserved Domains (1) summary
    smart00164
    Location:2111
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
  3. NM_001253914.1NP_001240843.1  TBC1 domain family member 1 isoform 3

    See identical proteins and their annotated locations for NP_001240843.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a large portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which has a significantly shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK074954, CR996632
    UniProtKB/TrEMBL
    Q8NC59
    Related
    ENST00000407365.5
    Conserved Domains (1) summary
    smart00164
    Location:2111
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
  4. NM_001253915.1NP_001240844.1  TBC1 domain family member 1 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a large portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (4) has a significantly shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK074954, BC032337, CR996632
    UniProtKB/TrEMBL
    Q8NC59
  5. NM_015173.4NP_055988.2  TBC1 domain family member 1 isoform 1

    See identical proteins and their annotated locations for NP_055988.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB449881, AK074954, BC014529, BC050321, DB036208
    Consensus CDS
    CCDS33972.1
    UniProtKB/Swiss-Prot
    Q86TI0
    UniProtKB/TrEMBL
    B9A6J6, Q6PJJ8, Q8NC59
    Related
    ENSP00000261439.4, ENST00000261439.9
    Conserved Domains (4) summary
    smart00164
    Location:7971014
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164371
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:695745
    DUF3350; Domain of unknown function (DUF3350)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    37891084..38139175
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513659.2XP_011511961.1  TBC1 domain family member 1 isoform X1

    Conserved Domains (5) summary
    smart00164
    Location:9241141
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:563871
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:822872
    DUF3350; Domain of unknown function (DUF3350)
  2. XM_011513660.3XP_011511962.1  TBC1 domain family member 1 isoform X2

    Conserved Domains (5) summary
    smart00164
    Location:9111128
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:563858
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:809859
    DUF3350; Domain of unknown function (DUF3350)
  3. XM_011513662.3XP_011511964.1  TBC1 domain family member 1 isoform X5

    Conserved Domains (4) summary
    smart00164
    Location:8841101
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:782832
    DUF3350; Domain of unknown function (DUF3350)
  4. XM_011513663.3XP_011511965.1  TBC1 domain family member 1 isoform X6

    Conserved Domains (4) summary
    smart00164
    Location:8711088
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:769819
    DUF3350; Domain of unknown function (DUF3350)
  5. XM_011513664.3XP_011511966.1  TBC1 domain family member 1 isoform X7

    Conserved Domains (4) summary
    smart00164
    Location:8701087
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:768818
    DUF3350; Domain of unknown function (DUF3350)
  6. XM_017007918.2XP_016863407.1  TBC1 domain family member 1 isoform X8

  7. XM_011513665.3XP_011511967.1  TBC1 domain family member 1 isoform X10

    Conserved Domains (4) summary
    smart00164
    Location:8301047
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:728778
    DUF3350; Domain of unknown function (DUF3350)
  8. XM_011513666.3XP_011511968.1  TBC1 domain family member 1 isoform X11

    Conserved Domains (4) summary
    smart00164
    Location:8171034
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:715765
    DUF3350; Domain of unknown function (DUF3350)
  9. XM_005262646.3XP_005262703.1  TBC1 domain family member 1 isoform X3

    See identical proteins and their annotated locations for XP_005262703.1

    Conserved Domains (5) summary
    smart00164
    Location:9041121
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164371
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:543851
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:802852
    DUF3350; Domain of unknown function (DUF3350)
  10. XM_005262647.3XP_005262704.1  TBC1 domain family member 1 isoform X4

    See identical proteins and their annotated locations for XP_005262704.1

    Conserved Domains (5) summary
    smart00164
    Location:8911108
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164371
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:543838
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:789839
    DUF3350; Domain of unknown function (DUF3350)
  11. XM_017007919.2XP_016863408.1  TBC1 domain family member 1 isoform X9

  12. XM_017007920.2XP_016863409.1  TBC1 domain family member 1 isoform X12

  13. XM_017007922.1XP_016863411.1  TBC1 domain family member 1 isoform X15

  14. XM_011513668.2XP_011511970.1  TBC1 domain family member 1 isoform X16

    Conserved Domains (3) summary
    cd00934
    Location:21150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:563788
    CytochromB561_N; Cytochrome B561, N terminal
  15. XM_005262649.3XP_005262706.1  TBC1 domain family member 1 isoform X13

    Conserved Domains (4) summary
    smart00164
    Location:775992
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd01269
    Location:35242
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:414722
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:673723
    DUF3350; Domain of unknown function (DUF3350)
  16. XM_017007921.2XP_016863410.1  TBC1 domain family member 1 isoform X14

  17. XM_006714001.3XP_006714064.1  TBC1 domain family member 1 isoform X17

    Conserved Domains (2) summary
    smart00164
    Location:175392
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam11830
    Location:73123
    DUF3350; Domain of unknown function (DUF3350)
  18. XM_011513670.3XP_011511972.1  TBC1 domain family member 1 isoform X18

    Related
    ENSP00000478039.1, ENST00000615497.4
    Conserved Domains (2) summary
    smart00164
    Location:123340
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam11830
    Location:2171
    DUF3350; Domain of unknown function (DUF3350)

RNA

  1. XR_001741181.1 RNA Sequence

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