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    ZSCAN9 zinc finger and SCAN domain containing 9 [ Homo sapiens (human) ]

    Gene ID: 7746, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZSCAN9provided by HGNC
    Official Full Name
    zinc finger and SCAN domain containing 9provided by HGNC
    Primary source
    HGNC:HGNC:12984
    See related
    Ensembl:ENSG00000137185 MIM:602246; AllianceGenome:HGNC:12984
    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
    PRD51; ZNF193
    Summary
    Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 5.8), endometrium (RPKM 3.5) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZSCAN9 in Genome Data Viewer
    Location:
    6p22.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (28225240..28233487)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28096976..28105223)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28193018..28201265)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:28180715-28181391 Neighboring gene tRNA-Ser (anticodon GCT) 5-1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28184762-28184955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24348 Neighboring gene transducer of ERBB2, 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24349 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:28203630-28204444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17042 Neighboring gene zinc finger with KRAB and SCAN domains 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17043 Neighboring gene NFKB activating protein like

    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. Upregulated expression of hITF in Crohn's disease and screening of hITF Interactant by a yeast two-hybrid system. Shi H, et al. Dig Dis Sci, 2010 Oct. PMID 20499178
    2. Three genes encoding zinc finger proteins on human chromosome 6p21.3: members of a new subclass of the Kruppel gene family containing the conserved SCAN box domain. Lee PL, et al. Genomics, 1997 Jul 15. PMID 9244436
    3. The zinc finger-associated SCAN box is a conserved oligomerization domain. Williams AJ, et al. Mol Cell Biol, 1999 Dec. PMID 10567577, Free PMC Article
    4. The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease. Butland SL, et al. Hum Mol Genet, 2014 Aug 1. PMID 24705354, Free PMC Article
    5. A Y2H-seq approach defines the human protein methyltransferase interactome. Weimann M, et al. Nat Methods, 2013 Apr. PMID 23455924

    See all (19) 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger and SCAN domain-containing protein 9
    Names
    cell proliferation-inducing gene 12 protein
    cell proliferation-inducing protein 12
    zinc finger protein 193

    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_001199479.2 → NP_001186408.1  zinc finger and SCAN domain-containing protein 9 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK226035, AK304013
      Consensus CDS
      CCDS56407.1
      UniProtKB/Swiss-Prot
      O15535
      Related
      ENSP00000404074.2, ENST00000425468.6
      Conserved Domains (6) summary
      smart00431
      Location:48 → 160
      SCAN; leucine rich region
      COG5048
      Location:304 → 440
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:307 → 327
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:305 → 327
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:49 → 136
      SCAN; SCAN domain
      pfam13465
      Location:320 → 344
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001199480.2 → NP_001186409.1  zinc finger and SCAN domain-containing protein 9 isoform 2

      See identical proteins and their annotated locations for NP_001186409.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks a segment in the 5' UTR and an in-frame exon in the CDS, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1. Variants 2 and 3 encode the same isoform 2.
      Source sequence(s)
      AK226035, AL022393, AU310237
      Consensus CDS
      CCDS4646.1
      UniProtKB/Swiss-Prot
      B4E1W6, E7EVQ2, O15535, Q2TTR1
      Related
      ENSP00000433402.1, ENST00000531979.5
      Conserved Domains (3) summary
      smart00431
      Location:48 → 160
      SCAN; leucine rich region
      COG5048
      Location:253 → 389
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:256 → 276
      ZF_C2H2; C2H2 Zn finger [structural motif]

    3. NM_001410841.1 → NP_001397770.1  zinc finger and SCAN domain-containing protein 9 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL022393
      Consensus CDS
      CCDS93875.1
      UniProtKB/TrEMBL
      A0A0B4J224
      Related
      ENSP00000433468.1, ENST00000527436.5

    4. NM_006299.5 → NP_006290.1  zinc finger and SCAN domain-containing protein 9 isoform 2

      See identical proteins and their annotated locations for NP_006290.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the CDS, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1. Variants 2 and 3 encode the same isoform 2.
      Source sequence(s)
      AK226035, AK304013, BC010374
      Consensus CDS
      CCDS4646.1
      UniProtKB/Swiss-Prot
      B4E1W6, E7EVQ2, O15535, Q2TTR1
      Related
      ENSP00000252207.5, ENST00000252207.10
      Conserved Domains (3) summary
      smart00431
      Location:48 → 160
      SCAN; leucine rich region
      COG5048
      Location:253 → 389
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:256 → 276
      ZF_C2H2; C2H2 Zn finger [structural motif]

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      28225240..28233487
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419316.1 → XP_047275272.1  zinc finger and SCAN domain-containing protein 9 isoform X1

    2. XM_011514878.3 → XP_011513180.1  zinc finger and SCAN domain-containing protein 9 isoform X4

      Conserved Domains (6) summary
      smart00431
      Location:180 → 292
      SCAN; leucine rich region
      COG5048
      Location:385 → 521
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:388 → 408
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:386 → 408
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:181 → 268
      SCAN; SCAN domain
      pfam13465
      Location:401 → 425
      zf-H2C2_2; Zinc-finger double domain

    3. XM_047419317.1 → XP_047275273.1  zinc finger and SCAN domain-containing protein 9 isoform X2

      Related
      ENSP00000436166.1, ENST00000527844.1

    4. XM_011514875.3 → XP_011513177.1  zinc finger and SCAN domain-containing protein 9 isoform X3

      Conserved Domains (6) summary
      smart00431
      Location:180 → 292
      SCAN; leucine rich region
      COG5048
      Location:442 → 578
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:445 → 465
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:443 → 465
      zf-C2H2; Zinc finger, C2H2 type
      pfam02023
      Location:181 → 268
      SCAN; SCAN domain
      pfam13465
      Location:458 → 482
      zf-H2C2_2; Zinc-finger double domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      28096976..28105223
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356357.1 → XP_054212332.1  zinc finger and SCAN domain-containing protein 9 isoform X6

    2. XM_054356356.1 → XP_054212331.1  zinc finger and SCAN domain-containing protein 9 isoform X2

    3. XM_054356354.1 → XP_054212329.1  zinc finger and SCAN domain-containing protein 9 isoform X5

    4. XM_054356355.1 → XP_054212330.1  zinc finger and SCAN domain-containing protein 9 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15535.1 GenPept UniProtKB/Swiss-Prot:O15535

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