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

Gene ID: 80317, updated on 18-Sep-2022

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 transcription, DNA-templated. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 1.5), ovary (RPKM 1.5) and 25 other tissues See more
Orthologs
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Genomic context

See ZKSCAN3 in Genome Data Viewer
Location:
6p22.1
Exon count:
8
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (28349878..28369172)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28221513..28240735)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28317724..28336949)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene piggyBac transposable element derived 1 Neighboring gene SMIM15 pseudogene 2 Neighboring gene zinc finger and SCAN domain containing 31 Neighboring gene zinc finger and SCAN domain containing 12 Neighboring gene uncharacterized LOC105374998

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

Homology

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
    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
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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
    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
    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
    28221513..28240735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)