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TTC39B tetratricopeptide repeat domain 39B [ Homo sapiens (human) ]

Gene ID: 158219, updated on 21-Dec-2019

Summary

Official Symbol
TTC39Bprovided by HGNC
Official Full Name
tetratricopeptide repeat domain 39Bprovided by HGNC
Primary source
HGNC:HGNC:23704
See related
Ensembl:ENSG00000155158 MIM:613574
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
C9orf52
Expression
Ubiquitous expression in kidney (RPKM 3.7), gall bladder (RPKM 3.5) and 25 other tissues See more
Orthologs

Genomic context

See TTC39B in Genome Data Viewer
Location:
9p22.3
Exon count:
27
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (15163622..15307360, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (15170842..15307358, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene PC4 and SFRS1 interacting protein 1 pseudogene 1 Neighboring gene uncharacterized LOC105375981 Neighboring gene RNA, U6 small nuclear 559, pseudogene Neighboring gene ribosomal protein L7 pseudogene 33 Neighboring gene RNA, U6 small nuclear 319, pseudogene Neighboring gene small nuclear RNA activating complex polypeptide 3

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 of seasonal pattern mania identifies NF1A as a possible susceptibility gene for bipolar disorder.
NHGRI GWA Catalog
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
NHGRI GWA Catalog
Biological, clinical and population relevance of 95 loci for blood lipids.
NHGRI GWA Catalog
Common variants at 30 loci contribute to polygenic dyslipidemia.
NHGRI GWA Catalog
Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels.
NHGRI GWA Catalog
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog
Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ33868

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cholesterol homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cholesterol homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
lipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cholesterol storage IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of cholesterol storage ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cholesterol efflux IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cholesterol efflux ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cholesterol metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cholesterol metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
tetratricopeptide repeat protein 39B
Names
TPR repeat protein 39B

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_001168339.1NP_001161811.1  tetratricopeptide repeat protein 39B isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AI473911, AK310271, AK310482, BC038592, BC142985, BX105862
    UniProtKB/Swiss-Prot
    Q5VTQ0
    Conserved Domains (2) summary
    pfam10300
    Location:142596
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:590656
    TPR_12; Tetratricopeptide repeat
  2. NM_001168340.1NP_001161812.1  tetratricopeptide repeat protein 39B isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has multiple differences in the central coding region but maintains the reading frame, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AK298998, AK310482, AL591393, BC142985
    Consensus CDS
    CCDS55296.1
    UniProtKB/Swiss-Prot
    Q5VTQ0
    Related
    ENSP00000370231.4, ENST00000380850.8
    Conserved Domains (3) summary
    sd00006
    Location:574606
    TPR; TPR repeat [structural motif]
    pfam10300
    Location:142585
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:579645
    TPR_12; Tetratricopeptide repeat
  3. NM_001168341.1NP_001161813.1  tetratricopeptide repeat protein 39B isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 4, which is shorter than isoform 1.
    Source sequence(s)
    AK298581, AK310271, AK310482, AL591393, BC042417, BC142985
    Consensus CDS
    CCDS55295.1
    UniProtKB/Swiss-Prot
    Q5VTQ0
    Related
    ENSP00000297615.5, ENST00000297615.9
    Conserved Domains (2) summary
    pfam10300
    Location:81529
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:523589
    TPR_12; Tetratricopeptide repeat
  4. NM_001168342.2NP_001161814.1  tetratricopeptide repeat protein 39B isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at an in-frame downstream AUG and result an isoform (5) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AI473911, AK301427, AK310271, AL591393, BC142985, BX105862, DT217817
    Consensus CDS
    CCDS55294.1
    UniProtKB/Swiss-Prot
    Q5VTQ0
    Related
    ENSP00000423392.1, ENST00000507993.5
    Conserved Domains (2) summary
    pfam10300
    Location:1433
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:429493
    TPR_12; Tetratricopeptide repeat
  5. NM_152574.2NP_689787.2  tetratricopeptide repeat protein 39B isoform 1

    See identical proteins and their annotated locations for NP_689787.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK091187, AK310482, AL591393, BC142985
    Consensus CDS
    CCDS6477.2
    UniProtKB/Swiss-Prot
    Q5VTQ0
    Related
    ENSP00000422496.1, ENST00000512701.6
    Conserved Domains (2) summary
    pfam10300
    Location:142598
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:592658
    TPR_12; Tetratricopeptide repeat

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    15163622..15307360 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447422.1XP_024303190.1  tetratricopeptide repeat protein 39B isoform X2

    Conserved Domains (2) summary
    pfam10300
    Location:45501
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:497561
    TPR_12; Tetratricopeptide repeat
  2. XM_017014311.1XP_016869800.1  tetratricopeptide repeat protein 39B isoform X2

    UniProtKB/Swiss-Prot
    Q5VTQ0
    Conserved Domains (2) summary
    pfam10300
    Location:45501
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:497561
    TPR_12; Tetratricopeptide repeat
  3. XM_017014310.1XP_016869799.1  tetratricopeptide repeat protein 39B isoform X1

  4. XM_024447423.1XP_024303191.1  tetratricopeptide repeat protein 39B isoform X2

    Conserved Domains (2) summary
    pfam10300
    Location:45501
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:497561
    TPR_12; Tetratricopeptide repeat
  5. XM_017014312.1XP_016869801.1  tetratricopeptide repeat protein 39B isoform X2

    UniProtKB/Swiss-Prot
    Q5VTQ0
    Conserved Domains (2) summary
    pfam10300
    Location:45501
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:497561
    TPR_12; Tetratricopeptide repeat
  6. XM_011517732.2XP_011516034.1  tetratricopeptide repeat protein 39B isoform X2

    UniProtKB/Swiss-Prot
    Q5VTQ0
    Conserved Domains (2) summary
    pfam10300
    Location:45501
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:497561
    TPR_12; Tetratricopeptide repeat
  7. XM_024447424.1XP_024303192.1  tetratricopeptide repeat protein 39B isoform X2

    Conserved Domains (2) summary
    pfam10300
    Location:45501
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:497561
    TPR_12; Tetratricopeptide repeat
  8. XM_024447425.1XP_024303193.1  tetratricopeptide repeat protein 39B isoform X3

    Related
    ENSP00000426539.1, ENST00000507285.5
    Conserved Domains (2) summary
    pfam10300
    Location:1433
    DUF3808; Protein of unknown function (DUF3808)
    pfam13424
    Location:429493
    TPR_12; Tetratricopeptide repeat

RNA

  1. XR_001746190.1 RNA Sequence

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