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

    Gene ID: 152877, updated on 4-Jan-2025

    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, Jan 2025]
    Expression
    Broad expression in testis (RPKM 2.2), thyroid (RPKM 0.5) and 15 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (1574062..1686017, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (1571319..1683894, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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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    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_001013622.3 → NP_001013644.1  protein FAM53A isoform 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

      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

      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_2024_08

    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

      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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    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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