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    AHCTF1 AT-hook containing transcription factor 1 [ Homo sapiens (human) ]

    Gene ID: 25909, updated on 5-May-2024

    Summary

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    Official Symbol
    AHCTF1provided by HGNC
    Official Full Name
    AT-hook containing transcription factor 1provided by HGNC
    Primary source
    HGNC:HGNC:24618
    See related
    Ensembl:ENSG00000153207 MIM:610853; AllianceGenome:HGNC:24618
    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
    ELYS; MST108; TMBS62; MSTP108
    Summary
    Predicted to enable DNA binding activity. Involved in nuclear pore complex assembly and regulation of cytokinesis. Located in nuclear membrane. Colocalizes with chromatin; kinetochore; and nuclear pore outer ring. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 25.0), bone marrow (RPKM 11.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q44
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (246839098..246931948, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (246270496..246363018, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (247002400..247095250, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:246939407-246940606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:246957595-246958236 Neighboring gene kinesin family member 28, pseudogene Neighboring gene long intergenic non-protein coding RNA 1341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2861 Neighboring gene MPRA-validated peak823 silencer Neighboring gene MPRA-validated peak824 silencer Neighboring gene MPRA-validated peak825 silencer Neighboring gene MPRA-validated peak826 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2863 Neighboring gene ZNF670-ZNF695 readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2865 Neighboring gene zinc finger protein 695 Neighboring gene Sharpr-MPRA regulatory region 11618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:247165417-247165917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2041 Neighboring gene zinc finger protein 519 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. The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity. Jevtić P, et al. EMBO Rep, 2019 Jun. PMID 31085625, Free PMC Article
    2. The nucleoporin ELYS/Mel28 regulates nuclear envelope subdomain formation in HeLa cells. Clever M, et al. Nucleus, 2012 Mar 1. PMID 22555603, Free PMC Article
    3. WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating. Scholz BA, et al. Nat Genet, 2019 Dec. PMID 31784729
    4. ELYS regulates the localization of LBR by modulating its phosphorylation state. Mimura Y, et al. J Cell Sci, 2016 Nov 15. PMID 27802161, Free PMC Article
    5. Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site. Chachoua I, et al. Nat Commun, 2022 Jan 11. PMID 35017527, Free PMC Article

    See all (85) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.
      Title: Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.
    2. we identify ELYS as a novel positive effector of mammalian nuclear size and propose that nuclear size is sensitive to NPC density and nuclear import capacity.
      Title: The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity.
    3. AHCTF1 regulates the super-enhancer-mediated gene gating process.The cancer-cell-specific gating of MYC is regulated by AHCTF1, which connects nucleoporins to the oncogenic super-enhancer via beta-catenin.
      Title: WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating.
    4. These observations point to a new mechanism regulating the localization of LBR, which is governed by an ELYS-mediated phosphorylation network.
      Title: ELYS regulates the localization of LBR by modulating its phosphorylation state.
    5. ELYS/Mel28 plays a role in NE subdomain formation in late mitosis
      Title: The nucleoporin ELYS/Mel28 regulates nuclear envelope subdomain formation in HeLa cells.
    6. Results suggets that ELYS is an unexpected member of the nuclear pore and kinetochore that functions in both pore assembly at the nucleus and faithful cell division.
      Title: ELYS is a dual nucleoporin/kinetochore protein required for nuclear pore assembly and proper cell division.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of AT hook containing transcription factor 1 (AHCTF1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • DKFZp434N093

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear pore complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nucleocytoplasmic transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cytokinesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    colocalizes_with kinetochore IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		  
    part_of nuclear pore IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of nuclear pore NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of nuclear pore outer ring IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein ELYS
    Names
    ELYS transcription factor-like protein TMBS62
    embryonic large molecule derived from yolk sac
    putative AT-hook-containing transcription factor 1

    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_001323342.2 → NP_001310271.1  protein ELYS isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC113174
      Consensus CDS
      CCDS91190.1
      UniProtKB/Swiss-Prot
      A6NGM0, A8MSG9, A8MZ86, Q7Z4E3, Q8IZA4, Q8WYP5, Q96EH9, Q9Y4Q6
      Related
      ENSP00000497061.2, ENST00000648844.2
      Conserved Domains (4) summary
      pfam09528
      Location:1637 → 2003
      Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)
      pfam13934
      Location:722 → 947
      ELYS; Nuclear pore complex assembly
      pfam16687
      Location:2 → 489
      ELYS-bb; beta-propeller of ELYS nucleoporin
      sd00039
      Location:223 → 259
      7WD40; WD40 repeat [structural motif]

    2. NM_001323343.2 → NP_001310272.1  protein ELYS isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC113174

    3. NM_001410950.1 → NP_001397879.1  protein ELYS isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC113174
      Consensus CDS
      CCDS91191.1
      Related
      ENSP00000355464.1, ENST00000366508.5

    4. NM_015446.5 → NP_056261.4  protein ELYS isoform 1

      Status: VALIDATED

      Source sequence(s)
      AB059277, AC113174, BC012307
      Consensus CDS
      CCDS1629.2
      UniProtKB/Swiss-Prot
      Q8WYP5
      Related
      ENSP00000355465.1, ENST00000326225.3
      Conserved Domains (4) summary
      pfam09528
      Location:1646 → 2012
      Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)
      pfam13934
      Location:731 → 956
      ELYS; Nuclear pore complex assembly
      pfam16687
      Location:11 → 498
      ELYS-bb; beta-propeller of ELYS nucleoporin
      sd00039
      Location:232 → 268
      7WD40; WD40 repeat [structural motif]

    RNA

    1. NR_136586.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC113174

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      246839098..246931948 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544157.4 → XP_011542459.3  protein ELYS isoform X2

    2. XM_011544156.3 → XP_011542458.3  protein ELYS isoform X1

    3. XM_047417231.1 → XP_047273187.1  protein ELYS isoform X3

    4. XM_047417232.1 → XP_047273188.1  protein ELYS isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      246270496..246363018 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335862.1 → XP_054191837.1  protein ELYS isoform X2

    2. XM_054335861.1 → XP_054191836.1  protein ELYS isoform X1

    3. XM_054335863.1 → XP_054191838.1  protein ELYS isoform X3

    4. XM_054335864.1 → XP_054191839.1  protein ELYS isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_175865.1: Suppressed sequence

      Description
      NM_175865.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WYP5.3 GenPept UniProtKB/Swiss-Prot:Q8WYP5

    Gene LinkOut

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

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