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

Gene ID: 80317, updated on 24-Nov-2020

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
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.
Expression
Ubiquitous expression in thyroid (RPKM 1.5), ovary (RPKM 1.5) and 25 other tissues See more
Orthologs

Genomic context

See ZKSCAN3 in Genome Data Viewer
Location:
6p22.1
Exon count:
8
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (28349913..28369174)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28317691..28336954)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene zinc finger and SCAN domain containing 26 Neighboring gene piggyBac transposable element derived 1 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

Associated conditions

Description Tests
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ33906, KIAA0426

Gene Ontology Provided by GOA

Process Evidence Code Pubs
autophagy IEA
Inferred from Electronic Annotation
more info
 
lysosome organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of autophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cellular senescence IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
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)

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
    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
    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 Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    28349913..28369174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715215.2XP_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
    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_006715216.2XP_006715279.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

    Conserved Domains (8) summary
    smart00431
    Location:42125
    SCAN; leucine rich region
    smart00349
    Location:185245
    KRAB; krueppel associated box
    COG5048
    Location:339486
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:343363
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:285307
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:188223
    KRAB; KRAB box
    pfam02023
    Location:42106
    SCAN; SCAN domain
    pfam13465
    Location:355380
    zf-H2C2_2; Zinc-finger double domain
  3. XM_017011320.1XP_016866809.1  zinc finger protein with KRAB and SCAN domains 3 isoform X2

    Conserved Domains (8) summary
    smart00431
    Location:42125
    SCAN; leucine rich region
    smart00349
    Location:185245
    KRAB; krueppel associated box
    COG5048
    Location:339486
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:343363
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:285307
    zf-C2H2; Zinc finger, C2H2 type
    pfam01352
    Location:188223
    KRAB; KRAB box
    pfam02023
    Location:42106
    SCAN; SCAN domain
    pfam13465
    Location:355380
    zf-H2C2_2; Zinc-finger double domain
  4. XM_005249423.3XP_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
  5. XM_006715218.3XP_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
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