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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
    mouse all
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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
    • 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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