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FAM53A family with sequence similarity 53 member A [ Homo sapiens (human) ]

Gene ID: 152877, updated on 5-Mar-2024

Summary

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Official Symbol
FAM53Aprovided by HGNC
Official Full Name
family with sequence similarity 53 member Aprovided by HGNC
Primary source
HGNC:HGNC:31860
See related
Ensembl:ENSG00000174137 MIM:617229; AllianceGenome:HGNC:31860
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
DNTNP
Summary
Predicted to be involved in protein import into nucleus. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 2.2), thyroid (RPKM 0.5) and 15 other tissues See more
Orthologs
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Genomic context

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See FAM53A in Genome Data Viewer
Location:
4p16.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (1574062..1686017, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (1571319..1683894, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (1641608..1686040, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 8056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1399591-1400181 Neighboring gene Sharpr-MPRA regulatory region 3424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1408939-1409612 Neighboring gene NK1 homeobox 1 Neighboring gene uncharacterized LOC105374348 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1513782-1514432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1522059-1522612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1545561-1546304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1546305-1547046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1550615-1551471 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1553567-1553737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1562577-1563106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1568111-1568928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1568929-1569747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1569748-1570565 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:1573296-1574073 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:1574074-1574850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1577987-1578860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1578861-1579734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1579735-1580607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15134 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:1582889-1583115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1595837-1596352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1600440-1601266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1605640-1606631 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1606632-1607622 Neighboring gene VISTA enhancer hs526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1616583-1617084 Neighboring gene uncharacterized LOC105374349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1648945-1649446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1686561-1687180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1687181-1687800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:1707982-1708482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21155 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:1723083-1724078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21156 Neighboring gene stem-loop histone mRNA binding protein Neighboring gene transmembrane protein 129, E3 ubiquitin ligase

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. TP53-based interaction analysis identifies cis-eQTL variants for TP53BP2, FBXO28, and FAM53A that associate with survival and treatment outcome in breast cancer. Fagerholm R, et al. Oncotarget, 2017 Mar 14. PMID 28179588, Free PMC Article
  2. Isolation of DNTNP, which encodes a potential nuclear protein that is expressed in the developing, dorsal neural tube. Jun L, et al. Dev Dyn, 2002 May. PMID 11984880
  3. A germline-specific class of small RNAs binds mammalian Piwi proteins. Girard A, et al. Nature, 2006 Jul 13. PMID 16751776
  4. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512
  5. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Fei T, et al. Proc Natl Acad Sci U S A, 2017 Jun 27. PMID 28611215, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Expression levels of TP53BP2, FBXO28, and FAM53A genes were associated with patient survival specifically in ER-positive, TP53-mutated tumors.
    Title: TP53-based interaction analysis identifies cis-eQTL variants for TP53BP2, FBXO28, and FAM53A that associate with survival and treatment outcome in breast cancer.
Submit: New GeneRIF Correction

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)

Genotypes

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

Process Evidence Code Pubs
involved_in protein import into nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein FAM53A
Names
dorsal neural-tube nuclear protein

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_001013622.3 → NP_001013644.1  protein FAM53A isoform 1

    See identical proteins and their annotated locations for NP_001013644.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AC016773, AC147067
    Consensus CDS
    CCDS33939.1
    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5
    Related
    ENSP00000426260.1, ENST00000472884.6
    Conserved Domains (1) summary
    pfam15242
    Location:1 → 294
    FAM53; Family of FAM53

  2. NM_001174070.3 → NP_001167541.1  protein FAM53A isoform 1

    See identical proteins and their annotated locations for NP_001167541.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AC147067, BC070112, HY040719
    Consensus CDS
    CCDS33939.1
    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5
    Related
    ENSP00000310057.6, ENST00000308132.11
    Conserved Domains (1) summary
    pfam15242
    Location:1 → 294
    FAM53; Family of FAM53

  3. NM_001297435.1 → NP_001284364.1  protein FAM53A isoform 2

    See identical proteins and their annotated locations for NP_001284364.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and contains an alternate exon in the central coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC147067, AK125566, BC042071
    Consensus CDS
    CCDS75091.1
    UniProtKB/TrEMBL
    C9JYQ7
    Related
    ENSP00000419044.1, ENST00000489363.5
    Conserved Domains (1) summary
    pfam15242
    Location:1 → 294
    FAM53; Family of FAM53

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    1574062..1686017 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449667.1 → XP_047305623.1  protein FAM53A isoform X4

  2. XM_047449670.1 → XP_047305626.1  protein FAM53A isoform X5

  3. XM_047449666.1 → XP_047305622.1  protein FAM53A isoform X3

  4. XM_047449669.1 → XP_047305625.1  protein FAM53A isoform X5

  5. XM_011513405.2 → XP_011511707.1  protein FAM53A isoform X5

    Conserved Domains (1) summary
    pfam15242
    Location:1 → 294
    FAM53; Family of FAM53

  6. XM_047449668.1 → XP_047305624.1  protein FAM53A isoform X5

  7. XM_024453912.2 → XP_024309680.1  protein FAM53A isoform X3

    Conserved Domains (1) summary
    pfam15242
    Location:1 → 294
    FAM53; Family of FAM53

  8. XM_047449671.1 → XP_047305627.1  protein FAM53A isoform X5

  9. XM_047449660.1 → XP_047305616.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  10. XM_047449662.1 → XP_047305618.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  11. XM_047449654.1 → XP_047305610.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  12. XM_047449655.1 → XP_047305611.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  13. XM_047449664.1 → XP_047305620.1  protein FAM53A isoform X2

    UniProtKB/TrEMBL
    C9JYQ7

  14. XM_047449657.1 → XP_047305613.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  15. XM_047449665.1 → XP_047305621.1  protein FAM53A isoform X2

    UniProtKB/TrEMBL
    C9JYQ7

  16. XM_011513402.3 → XP_011511704.1  protein FAM53A isoform X1

    See identical proteins and their annotated locations for XP_011511704.1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5
    Conserved Domains (1) summary
    pfam15242
    Location:1 → 294
    FAM53; Family of FAM53

  17. XM_047449663.1 → XP_047305619.1  protein FAM53A isoform X2

    UniProtKB/TrEMBL
    C9JYQ7

  18. XM_047449656.1 → XP_047305612.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  19. XM_047449661.1 → XP_047305617.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  20. XM_047449658.1 → XP_047305614.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  21. XM_047449659.1 → XP_047305615.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

RNA

  1. XR_007096374.1 RNA Sequence

  2. XR_924913.4 RNA Sequence

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021159990.1 Reference GRCh38.p14 PATCHES

    Range
    214780..232370 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    1571319..1683894 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349037.1 → XP_054205012.1  protein FAM53A isoform X4

  2. XM_054349041.1 → XP_054205016.1  protein FAM53A isoform X5

  3. XM_054349035.1 → XP_054205010.1  protein FAM53A isoform X3

  4. XM_054349040.1 → XP_054205015.1  protein FAM53A isoform X5

  5. XM_054349038.1 → XP_054205013.1  protein FAM53A isoform X5

  6. XM_054349039.1 → XP_054205014.1  protein FAM53A isoform X5

  7. XM_054349036.1 → XP_054205011.1  protein FAM53A isoform X3

  8. XM_054349042.1 → XP_054205017.1  protein FAM53A isoform X5

  9. XM_054349029.1 → XP_054205004.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  10. XM_054349031.1 → XP_054205006.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  11. XM_054349024.1 → XP_054204999.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  12. XM_054349025.1 → XP_054205000.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  13. XM_054349033.1 → XP_054205008.1  protein FAM53A isoform X2

    UniProtKB/TrEMBL
    C9JYQ7

  14. XM_054349027.1 → XP_054205002.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  15. XM_054349034.1 → XP_054205009.1  protein FAM53A isoform X2

    UniProtKB/TrEMBL
    C9JYQ7

  16. XM_054349028.1 → XP_054205003.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  17. XM_054349032.1 → XP_054205007.1  protein FAM53A isoform X2

    UniProtKB/TrEMBL
    C9JYQ7

  18. XM_054349026.1 → XP_054205001.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

  19. XM_054349030.1 → XP_054205005.1  protein FAM53A isoform X1

    UniProtKB/Swiss-Prot
    Q6NSI3, Q6ZUL5

RNA

  1. XR_008486931.1 RNA Sequence

  2. XR_008486932.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6NSI3.1 GenPept UniProtKB/Swiss-Prot:Q6NSI3

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