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BRINP3 BMP/retinoic acid inducible neural specific 3 [ Homo sapiens (human) ]

Gene ID: 339479, updated on 23-Nov-2023

Summary

Official Symbol
BRINP3provided by HGNC
Official Full Name
BMP/retinoic acid inducible neural specific 3provided by HGNC
Primary source
HGNC:HGNC:22393
See related
Ensembl:ENSG00000162670 MIM:618390; AllianceGenome:HGNC:22393
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FAM5C; DBCCR1L; DBCCR1L1
Summary
This gene is overexpressed in pituitary tumors but is underexpressed in tongue squamous cell carcinomas, ulcerative colitis, and peri-implantitis. Polymorphisms that increase expression of this gene have been shown to increase vascular inflammation, and an association of this gene with myocardial infarction has been demonstrated. Finally, hypermethylation of this gene may find usefulness as a biomarker for gastric cancer. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
Expression
Biased expression in brain (RPKM 4.5), small intestine (RPKM 2.0) and 6 other tissues See more
Orthologs
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Genomic context

See BRINP3 in Genome Data Viewer
Location:
1q31.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (190097658..190477864, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (189444081..189824968, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (190066788..190446994, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak549 silencer Neighboring gene long intergenic non-protein coding RNA 1701 Neighboring gene MPRA-validated peak550 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr1:189868671-189869595 Neighboring gene MPRA-validated peak553 silencer Neighboring gene DExH-box helicase 29 pseudogene Neighboring gene MPRA-validated peak555 silencer Neighboring gene MPRA-validated peak561 silencer Neighboring gene uncharacterized LOC105371659 Neighboring gene MPRA-validated peak564 silencer Neighboring gene MPRA-validated peak563 silencer Neighboring gene MPRA-validated peak566 silencer Neighboring gene uncharacterized LOC105371658 Neighboring gene MPRA-validated peak568 silencer Neighboring gene MPRA-validated peak569 silencer Neighboring gene MPRA-validated peak571 silencer Neighboring gene BRINP3 divergent transcript Neighboring gene MPRA-validated peak575 silencer Neighboring gene long intergenic non-protein coding RNA 1720 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:190647894-190649093 Neighboring gene MPRA-validated peak580 silencer

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 of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to retinoic acid IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cellular response to retinoic acid ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in central nervous system neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of mitotic cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of mitotic cell cycle ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in dendrite IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
 
is_active_in neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
BMP/retinoic acid-inducible neural-specific protein 3
Names
DBCCR1-like protein 1
bone morphogenetic protein/retinoic acid inducible neural-specific 3
family with sequence similarity 5, member C
protein FAM5C

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_001317188.2NP_001304117.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AK294365, AL365402, HY113909
    UniProtKB/Swiss-Prot
    Q76B58
    Conserved Domains (1) summary
    cl02616
    Location:39161
    MACPF; MAC/Perforin domain
  2. NM_199051.3NP_950252.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_950252.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB111893, AL365402, DA809835, DC330008
    Consensus CDS
    CCDS1373.1
    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
    Related
    ENSP00000356432.3, ENST00000367462.5
    Conserved Domains (2) summary
    smart00457
    Location:79263
    MACPF; membrane-attack complex / perforin
    pfam19052
    Location:319766
    BRINP; BMP/retinoic acid-inducible neural-specific protein

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    190097658..190477864 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017001129.2XP_016856618.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X4

    UniProtKB/Swiss-Prot
    Q76B58
    Conserved Domains (1) summary
    cl02616
    Location:39161
    MACPF; MAC/Perforin domain
  2. XM_017001127.2XP_016856616.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

    Conserved Domains (1) summary
    smart00457
    Location:50233
    MACPF; membrane-attack complex / perforin
  3. XM_017001126.2XP_016856615.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
    Conserved Domains (2) summary
    smart00457
    Location:79263
    MACPF; membrane-attack complex / perforin
    pfam19052
    Location:319766
    BRINP; BMP/retinoic acid-inducible neural-specific protein
  4. XM_017001125.2XP_016856614.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
    Conserved Domains (2) summary
    smart00457
    Location:79263
    MACPF; membrane-attack complex / perforin
    pfam19052
    Location:319766
    BRINP; BMP/retinoic acid-inducible neural-specific protein
  5. XM_047419250.1XP_047275206.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
  6. XM_017001128.2XP_016856617.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

    Conserved Domains (1) summary
    smart00457
    Location:50233
    MACPF; membrane-attack complex / perforin
  7. XM_011509476.3XP_011507778.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X4

    See identical proteins and their annotated locations for XP_011507778.1

    UniProtKB/Swiss-Prot
    Q76B58
    Conserved Domains (1) summary
    cl02616
    Location:39161
    MACPF; MAC/Perforin domain
  8. XM_047419245.1XP_047275201.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
  9. XM_011509472.3XP_011507774.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

    See identical proteins and their annotated locations for XP_011507774.1

    Conserved Domains (1) summary
    smart00457
    Location:50233
    MACPF; membrane-attack complex / perforin
  10. XM_011509475.3XP_011507777.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X3

    Conserved Domains (1) summary
    smart00457
    Location:37220
    MACPF; membrane-attack complex / perforin
  11. XM_017001133.2XP_016856622.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X6

  12. XM_017001132.2XP_016856621.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    189444081..189824968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336262.1XP_054192237.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
  2. XM_054336270.1XP_054192245.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X4

  3. XM_054336266.1XP_054192241.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

  4. XM_054336261.1XP_054192236.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
  5. XM_054336264.1XP_054192239.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
  6. XM_054336263.1XP_054192238.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
  7. XM_054336267.1XP_054192242.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

  8. XM_054336269.1XP_054192244.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X4

  9. XM_054336265.1XP_054192240.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X2

  10. XM_054336260.1XP_054192235.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KVP1, B7Z260, O95726, Q2M330, Q76B58
  11. XM_054336268.1XP_054192243.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X3

  12. XM_054336272.1XP_054192247.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X6

  13. XM_054336271.1XP_054192246.1  BMP/retinoic acid-inducible neural-specific protein 3 isoform X5