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    ATXN7L3 ataxin 7 like 3 [ Homo sapiens (human) ]

    Gene ID: 56970, updated on 5-Mar-2024

    Summary

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    Official Symbol
    ATXN7L3provided by HGNC
    Official Full Name
    ataxin 7 like 3provided by HGNC
    Primary source
    HGNC:HGNC:25416
    See related
    Ensembl:ENSG00000087152 MIM:619010; AllianceGenome:HGNC:25416
    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
    SGF11
    Summary
    Enables nuclear receptor coactivator activity. Involved in histone deubiquitination; histone monoubiquitination; and positive regulation of transcription, DNA-templated. Located in nucleus. Part of DUBm complex and SAGA complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in brain (RPKM 19.9), testis (RPKM 15.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATXN7L3 in Genome Data Viewer
    Location:
    17q21.31
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44191805..44199884, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (45044907..45052987, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42269173..42277252, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8576 Neighboring gene Sharpr-MPRA regulatory region 5 Neighboring gene homologous recombination factor with OB-fold Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12254 Neighboring gene ankyrin repeat and SOCS box containing 16 Neighboring gene ASB16 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42263664-42264198 Neighboring gene transmembrane and ubiquitin like domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42274223-42275146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42275147-42276069 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42276274-42276829 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42277555-42278093 Neighboring gene ATXN7L3 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42278094-42278631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42284331-42284831 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:42285473-42286672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8579 Neighboring gene Sharpr-MPRA regulatory region 7848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8581 Neighboring gene microRNA 6782 Neighboring gene upstream binding transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8582 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:42296769-42296933 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42299194-42299798 Neighboring gene SHC adaptor protein 1 pseudogene 2

    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. ATXN7L3 positively regulates SMAD7 transcription in hepatocellular carcinoma with growth inhibitory function. Sun N, et al. EBioMedicine, 2020 Dec. PMID 33186807, Free PMC Article
    2. Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL. Passet M, et al. Blood, 2022 Jun 16. PMID 35316324, Free PMC Article
    3. Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia. Kimura S, et al. Blood, 2022 Jun 16. PMID 35192684, Free PMC Article
    4. Long non-coding RNA DSCAM-AS1 contributes to the tumorigenesis of cervical cancer by targeting miR-877-5p/ATXN7L3 axis. Liang J, et al. Biosci Rep, 2020 Jan 31. PMID 31737900, Free PMC Article
    5. ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth. Atanassov BS, et al. Mol Cell, 2016 May 19. PMID 27132940, Free PMC Article

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL.
      Title: Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL.
    2. Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia.
      Title: Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia.
    3. ATXN7L3 positively regulates SMAD7 transcription in hepatocellular carcinoma with growth inhibitory function.
      Title: ATXN7L3 positively regulates SMAD7 transcription in hepatocellular carcinoma with growth inhibitory function.
    4. Long non-coding RNA DSCAM-AS1 contributes to the tumorigenesis of cervical cancer by targeting miR-877-5p/ATXN7L3 axis.
      Title: Long non-coding RNA DSCAM-AS1 contributes to the tumorigenesis of cervical cancer by targeting miR-877-5p/ATXN7L3 axis.
    5. ATXN7L3 and ENY2 orchestrate activities of multiple deubiquitinating enzymes, including USP27x and USP51, and that imbalances in these activities likely potentiate human diseases including cancer.
      Title: ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth.
    6. Downregulation of ATXN7L3 by short hairpin RNA speci fi cally inactivated the SAGA deubiquitination activity, leading to a strong increase of global H2B ubiquitination and a moderate increase of H2A ubiquitination.
      Title: The tightly controlled deubiquitination activity of the human SAGA complex differentially modifies distinct gene regulatory elements.
    7. The solution structures of the SCA7 domain of both ATXN7 and ATXN7L3 reveal a new, common zinc-finger motif at the heart of two distinct folds, providing a molecular basis for the observed functional differences.
      Title: The structural plasticity of SCA7 domains defines their differential nucleosome-binding properties.
    8. ATXN7L3, USP22, & ENY2 are required cofactors for full transcriptional activity by nuclear receptors. The deubiquitinase activity of TFTC/STAGA HAT counteracts heterochromatin silencing & is a positive cofactor for in vivo nuclear receptor activation.
      Title: A TFTC/STAGA module mediates histone H2A and H2B deubiquitination, coactivates nuclear receptors, and counteracts heterochromatin silencing.
    Submit: New GeneRIF Correction

    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)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp761G2113

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables nuclear receptor coactivator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of DNA repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of RNA splicing NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of DUBm complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of DUBm complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of SAGA complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of SAGA complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of SAGA complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of transcription factor TFTC complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ataxin-7-like protein 3

    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_001382308.1 → NP_001369237.1  ataxin-7-like protein 3 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1), as well as variant 3, encodes isoform a.
      Source sequence(s)
      AC004596
      Consensus CDS
      CCDS45697.1
      UniProtKB/TrEMBL
      K7EKG9
      Conserved Domains (2) summary
      pfam08209
      Location:80 → 112
      Sgf11; Sgf11 (transcriptional regulation protein)
      pfam08313
      Location:215 → 244
      SCA7; zinc-binding domain

    2. NM_001382309.1 → NP_001369238.1  ataxin-7-like protein 3 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2), as well as variants 4, 5, and 6, encodes isoform b.
      Source sequence(s)
      AC004596
      Consensus CDS
      CCDS42345.1
      UniProtKB/Swiss-Prot
      Q14CW9, Q8IY68, Q96N40, Q9NPU5
      UniProtKB/TrEMBL
      K7EKG9
      Related
      ENSP00000465614.2, ENST00000587097.6
      Conserved Domains (2) summary
      pfam08209
      Location:80 → 112
      Sgf11; Sgf11 (transcriptional regulation protein)
      pfam08313
      Location:208 → 237
      SCA7; zinc-binding domain

    3. NM_001382310.1 → NP_001369239.1  ataxin-7-like protein 3 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3), as well as variant 1, encodes isoform a.
      Source sequence(s)
      AC004596
      Consensus CDS
      CCDS45697.1
      UniProtKB/TrEMBL
      K7EKG9
      Related
      ENSP00000397259.1, ENST00000454077.6
      Conserved Domains (2) summary
      pfam08209
      Location:80 → 112
      Sgf11; Sgf11 (transcriptional regulation protein)
      pfam08313
      Location:215 → 244
      SCA7; zinc-binding domain

    4. NM_001382311.1 → NP_001369240.1  ataxin-7-like protein 3 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variants 2, 5, and 6, encodes isoform b.
      Source sequence(s)
      AC004596
      Consensus CDS
      CCDS42345.1
      UniProtKB/Swiss-Prot
      Q14CW9, Q8IY68, Q96N40, Q9NPU5
      UniProtKB/TrEMBL
      K7EKG9
      Related
      ENSP00000374035.3, ENST00000389384.8
      Conserved Domains (2) summary
      pfam08209
      Location:80 → 112
      Sgf11; Sgf11 (transcriptional regulation protein)
      pfam08313
      Location:208 → 237
      SCA7; zinc-binding domain

    5. NM_001382312.1 → NP_001369241.1  ataxin-7-like protein 3 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5), as well as variants 2, 4, and 6, encodes isoform b.
      Source sequence(s)
      AC004596
      Consensus CDS
      CCDS42345.1
      UniProtKB/Swiss-Prot
      Q14CW9, Q8IY68, Q96N40, Q9NPU5
      UniProtKB/TrEMBL
      K7EKG9
      Conserved Domains (2) summary
      pfam08209
      Location:80 → 112
      Sgf11; Sgf11 (transcriptional regulation protein)
      pfam08313
      Location:208 → 237
      SCA7; zinc-binding domain

    6. NM_001382313.1 → NP_001369242.1  ataxin-7-like protein 3 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6), as well as variants 2, 4, and 5, encodes isoform b.
      Source sequence(s)
      AC004596
      Consensus CDS
      CCDS42345.1
      UniProtKB/Swiss-Prot
      Q14CW9, Q8IY68, Q96N40, Q9NPU5
      UniProtKB/TrEMBL
      K7EKG9
      Conserved Domains (2) summary
      pfam08209
      Location:80 → 112
      Sgf11; Sgf11 (transcriptional regulation protein)
      pfam08313
      Location:208 → 237
      SCA7; zinc-binding domain

    7. NM_001382314.1 → NP_001369243.1  ataxin-7-like protein 3 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7), as well as variant 8, encodes isoform c.
      Source sequence(s)
      AC004596
      UniProtKB/TrEMBL
      K7EKG9
      Conserved Domains (2) summary
      pfam08209
      Location:87 → 119
      Sgf11; Sgf11 (transcriptional regulation protein)
      pfam08313
      Location:215 → 244
      SCA7; zinc-binding domain

    8. NM_001382315.1 → NP_001369244.1  ataxin-7-like protein 3 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8), as well as variant 7, encodes isoform c.
      Source sequence(s)
      AC004596
      UniProtKB/TrEMBL
      K7EKG9
      Conserved Domains (2) summary
      pfam08209
      Location:87 → 119
      Sgf11; Sgf11 (transcriptional regulation protein)
      pfam08313
      Location:215 → 244
      SCA7; zinc-binding domain

    9. NM_001382316.1 → NP_001369245.1  ataxin-7-like protein 3 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9), encodes the longest isoform (d).
      Source sequence(s)
      AC004596
      Conserved Domains (2) summary
      pfam08209
      Location:80 → 112
      Sgf11; Sgf11 (transcriptional regulation protein)
      pfam08313
      Location:227 → 256
      SCA7; zinc-binding domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      44191805..44199884 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      45044907..45052987 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001098833.1: Suppressed sequence

      Description
      NM_001098833.1: This RefSeq was removed because currently there is insufficient support for the transcript.

    2. NM_020218.1: Suppressed sequence

      Description
      NM_020218.1: This RefSeq was removed because currently there is insufficient support for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14CW9.1 GenPept UniProtKB/Swiss-Prot:Q14CW9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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