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TTC39A tetratricopeptide repeat domain 39A [ Homo sapiens (human) ]

Gene ID: 22996, updated on 14-Nov-2024

Summary

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Official Symbol
TTC39Aprovided by HGNC
Official Full Name
tetratricopeptide repeat domain 39Aprovided by HGNC
Primary source
HGNC:HGNC:18657
See related
Ensembl:ENSG00000085831 MIM:619885; AllianceGenome:HGNC:18657
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
DEME-6; C1orf34
Summary
Located in centrosome. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis (RPKM 15.4), colon (RPKM 9.3) and 14 other tissues See more
Orthologs
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Genomic context

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See TTC39A in Genome Data Viewer
Location:
1p32.3
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (51287258..51345116, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (51167163..51225015, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (51752930..51810788, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1562 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 873 Neighboring gene Sharpr-MPRA regulatory region 6511 Neighboring gene Sharpr-MPRA regulatory region 5693 Neighboring gene ring finger protein 11 Neighboring gene ribosomal protein S2 pseudogene 8 Neighboring gene uncharacterized LOC124904177 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:51763453-51764095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:51777239-51777740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:51777741-51778240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:51778629-51779444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1019 Neighboring gene TTC39A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 876 Neighboring gene proteasome 26S subunit, non-ATPase 7 pseudogene Neighboring gene epidermal growth factor receptor pathway substrate 15 Neighboring gene RNA, U6 small nuclear 877, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. Differential screening and suppression subtractive hybridization identified genes differentially expressed in an estrogen receptor-positive breast carcinoma cell line. Kuang WW, et al. Nucleic Acids Res, 1998 Feb 15. PMID 9461476, Free PMC Article
  2. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. Seki N, et al. DNA Res, 1997 Oct 31. PMID 9455484
  3. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. Wang AG, et al. Biochem Biophys Res Commun, 2006 Jul 7. PMID 16712791
  4. In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators. Franks JL, et al. PLoS Biol, 2020 Dec. PMID 33306668, Free PMC Article
  5. Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity. Kim JJ, et al. Genes Dev, 2019 Dec 1. PMID 31753913, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0452

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in centrosome IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
tetratricopeptide repeat protein 39A
Names
TPR repeat protein 39A
differentially expressed in MCF-7 with estradiol protein 6
differentially expressed in MCF7 with estradiol protein 6
testicular tissue protein Li 213

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)

  1. NM_001080494.3 → NP_001073963.1  tetratricopeptide repeat protein 39A isoform 2

    See identical proteins and their annotated locations for NP_001073963.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL162430, AL671986
    Consensus CDS
    CCDS44144.1
    UniProtKB/TrEMBL
    A0A140VJY6, B7Z4W9
    Related
    ENSP00000360815.5, ENST00000371750.9
    Conserved Domains (1) summary
    pfam10300
    Location:29 → 483
    DUF3808; Protein of unknown function (DUF3808)

  2. NM_001144832.2 → NP_001138304.1  tetratricopeptide repeat protein 39A isoform 1

    See identical proteins and their annotated locations for NP_001138304.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AF007170, BC028374, CX788693, DA871604
    Consensus CDS
    CCDS44143.1
    UniProtKB/TrEMBL
    B7Z4W9
    Related
    ENSP00000406144.2, ENST00000413473.6
    Conserved Domains (1) summary
    pfam10300
    Location:32 → 486
    DUF3808; Protein of unknown function (DUF3808)

  3. NM_001297662.2 → NP_001284591.1  tetratricopeptide repeat protein 39A isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains multiple differences, compared to variant 1, including initiation of translation at an alternate start codon. The encoded isoform (3) has distinct N- and C- termini and is shorter than isoform 1.
    Source sequence(s)
    AK000220
    Consensus CDS
    CCDS76163.1
    UniProtKB/TrEMBL
    A0A0A0MRQ0
    Related
    ENSP00000360812.3, ENST00000371747.7
    Conserved Domains (1) summary
    pfam10300
    Location:28 → 420
    DUF3808; Protein of unknown function (DUF3808)

  4. NM_001297663.2 → NP_001284592.1  tetratricopeptide repeat protein 39A isoform 4

    See identical proteins and their annotated locations for NP_001284592.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL162430, AL671986
    Consensus CDS
    CCDS90953.1
    UniProtKB/TrEMBL
    B7Z4W9
    Related
    ENSP00000505859.1, ENST00000680483.1
    Conserved Domains (1) summary
    pfam10300
    Location:28 → 482
    DUF3808; Protein of unknown function (DUF3808)

  5. NM_001297664.1 → NP_001284593.1  tetratricopeptide repeat protein 39A isoform 5

    See identical proteins and their annotated locations for NP_001284593.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (5) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AF007170, AK298019, BC028374, BI761577
    Consensus CDS
    CCDS72789.1
    UniProtKB/TrEMBL
    A0A0A0MSH8, A0A9K3Y803, A1LZS7, B7Z4W9, F6WE04
    Related
    ENSP00000262675.7, ENST00000262675.11
    Conserved Domains (1) summary
    pfam10300
    Location:1 → 455
    DUF3808; Protein of unknown function (DUF3808)

  6. NM_001297665.1 → NP_001284594.1  tetratricopeptide repeat protein 39A isoform 6

    See identical proteins and their annotated locations for NP_001284594.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains multiple differences, compared to variant 1, including initiation of translation at an alternate start codon. The encoded isoform (6) has a distinct N-terminus and is longer than isoform 1.
    Source sequence(s)
    AF007170, AK000220, BC028374, HY029911
    Consensus CDS
    CCDS72790.1
    UniProtKB/Swiss-Prot
    B7Z782, E7EQY9, G3XAF8, O43417, O75040, Q5SRH5, Q5SRH6, Q5SRH7, Q5SRH8, Q5SRH9, Q5SRI0, Q5SRI1, Q5SRI2, Q5T7S1, Q6PIU8, Q9BT24
    UniProtKB/TrEMBL
    B7Z4W9
    Related
    ENSP00000393952.2, ENST00000447632.6
    Conserved Domains (1) summary
    pfam10300
    Location:29 → 518
    DUF3808; Protein of unknown function (DUF3808)

  7. NM_001297666.1 → NP_001284595.1  tetratricopeptide repeat protein 39A isoform 7

    See identical proteins and their annotated locations for NP_001284595.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) 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 (7) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AF007170, BC004399, BQ227134
    Consensus CDS
    CCDS76162.1
    UniProtKB/Swiss-Prot
    Q5SRH9
    Related
    ENSP00000431228.1, ENST00000530004.5
    Conserved Domains (1) summary
    pfam10300
    Location:1 → 126
    DUF3808; Protein of unknown function (DUF3808)

  8. NM_001297667.1 → NP_001284596.1  tetratricopeptide repeat protein 39A isoform 8

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) 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 (8) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AF007170, BQ227134
    UniProtKB/Swiss-Prot
    Q5SRH9
    Conserved Domains (1) summary
    pfam10300
    Location:1 → 59
    DUF3808; Protein of unknown function (DUF3808)

  9. NM_001410793.1 → NP_001397722.1  tetratricopeptide repeat protein 39A isoform 9

    Status: VALIDATED

    Source sequence(s)
    AL162430, AL671986
    Consensus CDS
    CCDS90954.1
    UniProtKB/TrEMBL
    A0A0A0MSW9
    Related
    ENSP00000405803.2, ENST00000439482.6

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    51287258..51345116 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541048.3 → XP_011539350.1  tetratricopeptide repeat protein 39A isoform X1

    UniProtKB/TrEMBL
    B7Z4W9
    Conserved Domains (1) summary
    pfam10300
    Location:32 → 521
    DUF3808; Protein of unknown function (DUF3808)

  2. XM_011541053.3 → XP_011539355.1  tetratricopeptide repeat protein 39A isoform X5

    See identical proteins and their annotated locations for XP_011539355.1

    UniProtKB/TrEMBL
    A0A7P0T922, B7Z4W9
    Conserved Domains (1) summary
    pfam10300
    Location:1 → 490
    DUF3808; Protein of unknown function (DUF3808)

  3. XM_005270644.3 → XP_005270701.1  tetratricopeptide repeat protein 39A isoform X6

    UniProtKB/TrEMBL
    B7Z4W9
    Conserved Domains (1) summary
    pfam10300
    Location:25 → 479
    DUF3808; Protein of unknown function (DUF3808)

  4. XM_006710471.3 → XP_006710534.1  tetratricopeptide repeat protein 39A isoform X3

    UniProtKB/TrEMBL
    B7Z4W9
    Conserved Domains (1) summary
    pfam10300
    Location:25 → 514
    DUF3808; Protein of unknown function (DUF3808)

  5. XM_011541051.3 → XP_011539353.1  tetratricopeptide repeat protein 39A isoform X5

    See identical proteins and their annotated locations for XP_011539353.1

    UniProtKB/TrEMBL
    A0A7P0T922, B7Z4W9
    Conserved Domains (1) summary
    pfam10300
    Location:1 → 490
    DUF3808; Protein of unknown function (DUF3808)

  6. XM_047449644.1 → XP_047305600.1  tetratricopeptide repeat protein 39A isoform X8

    UniProtKB/TrEMBL
    A0A0A0MSH8, A0A9K3Y803, A1LZS7, F6WE04

  7. XM_047449632.1 → XP_047305588.1  tetratricopeptide repeat protein 39A isoform X5

    UniProtKB/TrEMBL
    A0A7P0T922

  8. XM_047449641.1 → XP_047305597.1  tetratricopeptide repeat protein 39A isoform X7

  9. XM_047449631.1 → XP_047305587.1  tetratricopeptide repeat protein 39A isoform X4

  10. XM_011541054.3 → XP_011539356.1  tetratricopeptide repeat protein 39A isoform X8

    See identical proteins and their annotated locations for XP_011539356.1

    UniProtKB/TrEMBL
    A0A0A0MSH8, A0A9K3Y803, A1LZS7, B7Z4W9, F6WE04
    Related
    ENSP00000388995.2, ENST00000422925.6
    Conserved Domains (1) summary
    pfam10300
    Location:1 → 455
    DUF3808; Protein of unknown function (DUF3808)

  11. XM_011541052.3 → XP_011539354.1  tetratricopeptide repeat protein 39A isoform X5

    See identical proteins and their annotated locations for XP_011539354.1

    UniProtKB/TrEMBL
    A0A7P0T922, B7Z4W9
    Related
    ENSP00000505465.1, ENST00000680290.1
    Conserved Domains (1) summary
    pfam10300
    Location:1 → 490
    DUF3808; Protein of unknown function (DUF3808)

  12. XM_011541049.3 → XP_011539351.1  tetratricopeptide repeat protein 39A isoform X2

    UniProtKB/TrEMBL
    B7Z4W9
    Conserved Domains (1) summary
    pfam10300
    Location:30 → 519
    DUF3808; Protein of unknown function (DUF3808)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    51167163..51225015 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335239.1 → XP_054191214.1  tetratricopeptide repeat protein 39A isoform X1

  2. XM_054335246.1 → XP_054191221.1  tetratricopeptide repeat protein 39A isoform X5

    UniProtKB/TrEMBL
    A0A7P0T922

  3. XM_054335241.1 → XP_054191216.1  tetratricopeptide repeat protein 39A isoform X3

  4. XM_054335247.1 → XP_054191222.1  tetratricopeptide repeat protein 39A isoform X6

  5. XM_054335245.1 → XP_054191220.1  tetratricopeptide repeat protein 39A isoform X5

    UniProtKB/TrEMBL
    A0A7P0T922

  6. XM_054335250.1 → XP_054191225.1  tetratricopeptide repeat protein 39A isoform X8

    UniProtKB/TrEMBL
    A0A0A0MSH8, A0A9K3Y803, A1LZS7, F6WE04

  7. XM_054335243.1 → XP_054191218.1  tetratricopeptide repeat protein 39A isoform X5

    UniProtKB/TrEMBL
    A0A7P0T922

  8. XM_054335248.1 → XP_054191223.1  tetratricopeptide repeat protein 39A isoform X7

  9. XM_054335242.1 → XP_054191217.1  tetratricopeptide repeat protein 39A isoform X4

  10. XM_054335244.1 → XP_054191219.1  tetratricopeptide repeat protein 39A isoform X5

    UniProtKB/TrEMBL
    A0A7P0T922

  11. XM_054335249.1 → XP_054191224.1  tetratricopeptide repeat protein 39A isoform X8

    UniProtKB/TrEMBL
    A0A0A0MSH8, A0A9K3Y803, A1LZS7, F6WE04

  12. XM_054335240.1 → XP_054191215.1  tetratricopeptide repeat protein 39A isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5SRH9.1 GenPept UniProtKB/Swiss-Prot:Q5SRH9

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