U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    ZKSCAN3 zinc finger with KRAB and SCAN domains 3 [ Homo sapiens (human) ]

    Gene ID: 80317, updated on 9-Dec-2024

    Summary

    Official Symbol
    ZKSCAN3provided by HGNC
    Official Full Name
    zinc finger with KRAB and SCAN domains 3provided by HGNC
    Primary source
    HGNC:HGNC:13853
    See related
    Ensembl:ENSG00000189298 MIM:612791; AllianceGenome:HGNC:13853
    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
    ZF47; Zfp47; ZFP306; ZNF306; ZNF309; zfp-47; ZSCAN13; ZSCAN35; dJ874C20.1; dJ874C20.1.
    Summary
    Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in several processes, including negative regulation of autophagy; negative regulation of cellular senescence; and regulation of DNA-templated transcription. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 1.5), ovary (RPKM 1.5) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See ZKSCAN3 in Genome Data Viewer
    Location:
    6p22.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (28349878..28369172)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28221444..28240735)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28317724..28336949)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17044 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28249721-28249897 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:28251848-28252055 Neighboring gene piggyBac transposable element derived 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28278749-28279250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28279251-28279750 Neighboring gene SMIM15 pseudogene 2 Neighboring gene zinc finger and SCAN domain containing 31 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:28321865-28322364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24355 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:28324191-28325095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24356 Neighboring gene zinc finger and SCAN domain containing 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17045 Neighboring gene uncharacterized LOC105374998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24357

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ33906, KIAA0426

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in cytoplasm 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

    Preferred Names
    zinc finger protein with KRAB and SCAN domains 3
    Names
    zinc finger and SCAN domain-containing protein 13
    zinc finger protein 306
    zinc finger protein 309
    zinc finger protein 47 homolog
    zinc finger protein zfp47

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001242894.2NP_001229823.1  zinc finger protein with KRAB and SCAN domains 3 isoform 1

      See identical proteins and their annotated locations for NP_001229823.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK313532, AL021997, AL358785, DA440043
      Consensus CDS
      CCDS4650.1
      UniProtKB/Swiss-Prot
      B2R8W2, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9BRR0, Q9H4T3
      Related
      ENSP00000366465.1, ENST00000377255.3
      Conserved Domains (8) summary
      smart00431
      Location:42154
      SCAN; leucine rich region
      smart00349
      Location:214274
      KRAB; krueppel associated box
      COG5048
      Location:368515
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:372392
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:314336
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:217252
      KRAB; KRAB box
      pfam02023
      Location:42130
      SCAN; SCAN domain
      pfam13465
      Location:384409
      zf-H2C2_2; Zinc-finger double domain
    2. NM_001242895.2NP_001229824.1  zinc finger protein with KRAB and SCAN domains 3 isoform 2

      See identical proteins and their annotated locations for NP_001229824.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 1. The resulting protein (isoform 2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK122790, AL021997, AL358785, DA440043
      Consensus CDS
      CCDS56408.1
      UniProtKB/Swiss-Prot
      Q9BRR0
      Related
      ENSP00000341883.5, ENST00000341464.9
      Conserved Domains (6) summary
      smart00349
      Location:66126
      KRAB; krueppel associated box
      COG5048
      Location:220367
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:224244
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:166188
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:69104
      KRAB; KRAB box
      pfam13465
      Location:236261
      zf-H2C2_2; Zinc-finger double domain
    3. NM_024493.4NP_077819.2  zinc finger protein with KRAB and SCAN domains 3 isoform 1

      See identical proteins and their annotated locations for NP_077819.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein (isoform 1).
      Source sequence(s)
      AL021997, AL358785, BC006118, DA440043
      Consensus CDS
      CCDS4650.1
      UniProtKB/Swiss-Prot
      B2R8W2, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9BRR0, Q9H4T3
      Related
      ENSP00000252211.2, ENST00000252211.7
      Conserved Domains (8) summary
      smart00431
      Location:42154
      SCAN; leucine rich region
      smart00349
      Location:214274
      KRAB; krueppel associated box
      COG5048
      Location:368515
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:372392
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:314336
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:217252
      KRAB; KRAB box
      pfam02023
      Location:42130
      SCAN; SCAN domain
      pfam13465
      Location:384409
      zf-H2C2_2; Zinc-finger double domain

    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
      28349878..28369172
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006715215.3XP_006715278.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      See identical proteins and their annotated locations for XP_006715278.1

      UniProtKB/Swiss-Prot
      B2R8W2, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9BRR0, Q9H4T3
      Conserved Domains (8) summary
      smart00431
      Location:42154
      SCAN; leucine rich region
      smart00349
      Location:214274
      KRAB; krueppel associated box
      COG5048
      Location:368515
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:372392
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:314336
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:217252
      KRAB; KRAB box
      pfam02023
      Location:42130
      SCAN; SCAN domain
      pfam13465
      Location:384409
      zf-H2C2_2; Zinc-finger double domain
    2. XM_047419375.1XP_047275331.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

    3. XM_047419376.1XP_047275332.1  zinc finger protein with KRAB and SCAN domains 3 isoform X4

    4. XM_047419373.1XP_047275329.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

      UniProtKB/Swiss-Prot
      B2R8W2, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9BRR0, Q9H4T3
    5. XM_047419374.1XP_047275330.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

    6. XM_005249423.4XP_005249480.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

      Conserved Domains (6) summary
      smart00349
      Location:81141
      KRAB; krueppel associated box
      COG5048
      Location:235382
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:239259
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:181203
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:84119
      KRAB; KRAB box
      pfam13465
      Location:251276
      zf-H2C2_2; Zinc-finger double domain
    7. XM_006715218.4XP_006715281.1  zinc finger protein with KRAB and SCAN domains 3 isoform X4

      See identical proteins and their annotated locations for XP_006715281.1

      UniProtKB/Swiss-Prot
      Q9BRR0
      Conserved Domains (6) summary
      smart00349
      Location:66126
      KRAB; krueppel associated box
      COG5048
      Location:220367
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:224244
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:166188
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:69104
      KRAB; KRAB box
      pfam13465
      Location:236261
      zf-H2C2_2; Zinc-finger double domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      28221444..28240735
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356459.1XP_054212434.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

    2. XM_054356462.1XP_054212437.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

    3. XM_054356460.1XP_054212435.1  zinc finger protein with KRAB and SCAN domains 3 isoform X1

    4. XM_054356461.1XP_054212436.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

    5. XM_054356464.1XP_054212439.1  zinc finger protein with KRAB and SCAN domains 3 isoform X4

    6. XM_054356463.1XP_054212438.1  zinc finger protein with KRAB and SCAN domains 3 isoform X3

    7. XM_054356465.1XP_054212440.1  zinc finger protein with KRAB and SCAN domains 3 isoform X4