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SCAND3 SCAN domain containing 3 [ Homo sapiens (human) ]

Gene ID: 114821, updated on 3-Apr-2024

Summary

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Official Symbol
SCAND3provided by HGNC
Official Full Name
SCAN domain containing 3provided by HGNC
Primary source
HGNC:HGNC:13851
See related
Ensembl:ENSG00000232040 MIM:615254; AllianceGenome:HGNC:13851
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
ZBED9; ZNF452; Buster4; FAM200D; ZFP38-L; ZNF305P2; dJ1186N24.3
Summary
Predicted to enable nucleic acid binding activity. Involved in positive regulation of cell cycle and positive regulation of epithelial cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis (RPKM 5.0), thyroid (RPKM 0.8) and 7 other tissues See more
Orthologs
all
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Genomic context

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Location:
6p22.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (28570535..28616202, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (28441914..28487574, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (28538312..28583979, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene tRNA-Ile (anticodon TAT) 3-1 Neighboring gene uncharacterized LOC107986586 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:28511751-28512333 Neighboring gene tRNA-Arg (anticodon TCG) 5-1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:28554695-28555571 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:28557063-28557742 Neighboring gene ZBED9 antisense RNA 1 Neighboring gene tRNA-Gln (anticodon TTG) 2-1 Neighboring gene tRNA-Ser (anticodon GCT) 4-1 Neighboring gene tRNA-Ala (anticodon AGC) 3-1 Neighboring gene tRNA-Ala (anticodon TGC) 9-1 Neighboring gene uncharacterized LOC105374996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:28607773-28608273 Neighboring gene tRNA-Ala (anticodon TGC) 2-1

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 AGT epistasis pattern proposed a novel role for ZBED9 in regulating blood pressure: Tehran Cardiometabolic genetic study (TCGS). Akbarzadeh M, et al. Gene, 2022 Jul 15. PMID 35577038
  2. Genome-wide association study on blood pressure traits in the Iranian population suggests ZBED9 as a new locus for hypertension. Kolifarhood G, et al. Sci Rep, 2021 Jun 3. PMID 34083597, Free PMC Article
  3. ZNF452 facilitates tumor proliferation and invasion via activating AKT-GSK3β signaling pathway and predicts poor prognosis of non-small cell lung cancer patients. Zhang X, et al. Oncotarget, 2017 Jun 13. PMID 28418919, Free PMC Article
  4. On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain. Llorens C, et al. Mob Genet Elements, 2012 Sep 1. PMID 23550032, Free PMC Article
  5. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. Hayward A, et al. PLoS One, 2013. PMID 23533661, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The AGT epistasis pattern proposed a novel role for ZBED9 in regulating blood pressure: Tehran Cardiometabolic genetic study (TCGS).
    Title: The AGT epistasis pattern proposed a novel role for ZBED9 in regulating blood pressure: Tehran Cardiometabolic genetic study (TCGS).
  2. Genome-wide association study on blood pressure traits in the Iranian population suggests ZBED9 as a new locus for hypertension.
    Title: Genome-wide association study on blood pressure traits in the Iranian population suggests ZBED9 as a new locus for hypertension.
  3. the present study indicated that ZNF452 may be an upstream regulator of AKT-GSK3beta signaling pathway and facilitates proliferation and invasion of non-small cell lung cancer
    Title: ZNF452 facilitates tumor proliferation and invasion via activating AKT-GSK3β signaling pathway and predicts poor prognosis of non-small cell lung cancer patients.
Submit: New GeneRIF Correction

Phenotypes

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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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ31087, KIAA1925, MGC131782, MGC133310, MGC133311, DKFZp434N092

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA integration IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of epithelial cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
SCAN domain-containing protein 3
Names
transposon-derived Buster4 transposase-like protein
zinc finger BED domain-containing protein 9
zinc finger BED-type containing 9
zinc finger protein 305 pseudogene 2
zinc finger protein 452

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_001329616.2 → NP_001316545.1  SCAN domain-containing protein 3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AL049543, AL121932, AY517631, DB636313
    Consensus CDS
    CCDS87376.1
    UniProtKB/TrEMBL
    A0A1U9X8V2, A0A1U9X8V6, A0A2R8Y5N3
    Conserved Domains (4) summary
    pfam05699
    Location:1097 → 1144
    Dimer_Tnp_hAT; hAT family C-terminal dimerization region
    pfam10481
    Location:274 → 416
    CENP-F_N; Cenp-F N-terminal domain
    pfam14291
    Location:731 → 828
    DUF4371; Domain of unknown function (DUF4371)
    cl21549
    Location:225 → 325
    rve; Integrase core domain

  2. NM_052923.2 → NP_443155.1  SCAN domain-containing protein 3 isoform 1

    See identical proteins and their annotated locations for NP_443155.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL049543, AY517631
    Consensus CDS
    CCDS34355.1
    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8V2, A0A1U9X8V6, A0A1U9X8W9
    Related
    ENSP00000395259.2, ENST00000452236.3
    Conserved Domains (2) summary
    smart00431
    Location:48 → 160
    SCAN; leucine rich region
    cl21549
    Location:376 → 476
    rve; Integrase core domain

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    28570535..28616202 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514287.3 → XP_011512589.1  SCAN domain-containing protein 3 isoform X2

    See identical proteins and their annotated locations for XP_011512589.1

    UniProtKB/TrEMBL
    A0A1U9X8V2, A0A1U9X8V6, A0A2R8Y5N3
    Related
    ENSP00000494942.1, ENST00000646382.1
    Conserved Domains (4) summary
    pfam05699
    Location:1097 → 1144
    Dimer_Tnp_hAT; hAT family C-terminal dimerization region
    pfam10481
    Location:274 → 416
    CENP-F_N; Cenp-F N-terminal domain
    pfam14291
    Location:731 → 828
    DUF4371; Domain of unknown function (DUF4371)
    cl21549
    Location:225 → 325
    rve; Integrase core domain

  2. XM_047418158.1 → XP_047274114.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  3. XM_047418156.1 → XP_047274112.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  4. XM_047418157.1 → XP_047274113.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  5. XM_011514288.3 → XP_011512590.1  SCAN domain-containing protein 3 isoform X3

    See identical proteins and their annotated locations for XP_011512590.1

    UniProtKB/TrEMBL
    A0A1U9X8V2, A0A1U9X8V6
    Conserved Domains (4) summary
    pfam05699
    Location:1052 → 1099
    Dimer_Tnp_hAT; hAT family C-terminal dimerization region
    pfam10481
    Location:229 → 371
    CENP-F_N; Cenp-F N-terminal domain
    pfam14291
    Location:686 → 783
    DUF4371; Domain of unknown function (DUF4371)
    cl21549
    Location:180 → 280
    rve; Integrase core domain

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    60416..106077 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329735.1 → XP_054185710.1  SCAN domain-containing protein 3 isoform X2

    UniProtKB/TrEMBL
    A0A2R8Y5N3

  2. XM_054329734.1 → XP_054185709.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  3. XM_054329731.1 → XP_054185706.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  4. XM_054329732.1 → XP_054185707.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  5. XM_054329733.1 → XP_054185708.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    28441914..28487574 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354177.1 → XP_054210152.1  SCAN domain-containing protein 3 isoform X2

    UniProtKB/TrEMBL
    A0A2R8Y5N3

  2. XM_054354176.1 → XP_054210151.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  3. XM_054354173.1 → XP_054210148.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  4. XM_054354174.1 → XP_054210149.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  5. XM_054354175.1 → XP_054210150.1  SCAN domain-containing protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q2NKL9, Q5SRJ3, Q6R2W3, Q8TCN2, Q96MV9, Q96PW3
    UniProtKB/TrEMBL
    A0A1U9X8W9

  6. XM_054354178.1 → XP_054210153.1  SCAN domain-containing protein 3 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6R2W3.1 GenPept UniProtKB/Swiss-Prot:Q6R2W3

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