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nitr4a novel immune-type receptor 4a [ Danio rerio (zebrafish) ]

Gene ID: 60652, updated on 4-Jan-2025

Summary

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Official Symbol
nitr4aprovided by ZNC
Official Full Name
novel immune-type receptor 4aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-001106-11
See related
Ensembl:ENSDARG00000075288 AllianceGenome:ZFIN:ZDB-GENE-001106-11
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
nitr; nitr4a_9; dZ105L16.2; dZ105L16.3; dZ105L16.8
Summary
Predicted to be involved in response to bacterium. Predicted to be located in plasma membrane. Is expressed in intestine; kidney; and spleen. Orthologous to human SIRPB2 (signal regulatory protein beta 2). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
all
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Genomic context

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See nitr4a in Genome Data Viewer
Location:
chromosome: 7
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (17578061..17582292, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (17326085..17330335, complement)

Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene novel immune-type receptor 3d Neighboring gene novel immune-type receptor 1n Neighboring gene novel immune-type receptor 5 Neighboring gene novel immune-type receptor 4b, pseudogene Neighboring gene novel immune-type receptor 6a Neighboring gene novel immune-type receptor 6b

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Evolution of the zebrafish model: from development to immunity and infectious disease. Phelps HA, et al. Zebrafish, 2005. PMID 18248169
  2. Developmental and tissue-specific expression of NITRs. Yoder JA, et al. Immunogenetics, 2010 Feb. PMID 20012603, Free PMC Article
  3. The medaka novel immune-type receptor (NITR) gene clusters reveal an extraordinary degree of divergence in variable domains. Desai S, et al. BMC Evol Biol, 2008 Jun 19. PMID 18565225, Free PMC Article
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by ZFIN

Process Evidence Code Pubs
involved_in response to bacterium IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
novel immune-type receptor 4a

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_131654.1 → NP_571729.1  novel immune-type receptor 4a isoform 1 precursor

    See identical proteins and their annotated locations for NP_571729.1

    Status: PROVISIONAL

    Description
    Transcript Variant: This variant (1, also known as nitr4a-1 allele) differs in the 3' UTR compared to variant 6, and encodes isoform 1. Variants 1, 2, 3 and 6 encode isoforms of the same length that differ in their amino acid composition.
    Source sequence(s)
    AF318402
    UniProtKB/TrEMBL
    Q8UV83, Q90Z85
    Conserved Domains (3) summary
    smart00410
    Location:29 → 127
    IG_like; Immunoglobulin like
    pfam07686
    Location:144 → 246
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:24 → 134
    Ig; Immunoglobulin domain

  2. NM_131655.1 → NP_571730.1  novel immune-type receptor 4a isoform 2 precursor

    See identical proteins and their annotated locations for NP_571730.1

    Status: PROVISIONAL

    Description
    Transcript Variant: This variant (2, also known as nitr4a-2 allele) differs in the 3' UTR compared to variant 6, and encodes isoform 2. Variants 1, 2, 3 and 6 encode isoforms of the same length that differ in their amino acid composition.
    Source sequence(s)
    AF318403
    UniProtKB/TrEMBL
    Q8UV83, Q90Z84
    Conserved Domains (3) summary
    smart00410
    Location:146 → 246
    IG_like; Immunoglobulin like
    pfam07686
    Location:144 → 246
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:24 → 134
    Ig; Immunoglobulin domain

  3. NM_131656.1 → NP_571731.1  novel immune-type receptor 4a isoform 3 precursor

    See identical proteins and their annotated locations for NP_571731.1

    Status: PROVISIONAL

    Description
    Transcript Variant: This variant (3, also known as nitr4a-3 allele) differs in the 3' UTR compared to variant 6, and encodes isoform 3. Variants 1, 2, 3 and 6 encode isoforms of the same length that differ in their amino acid composition.
    Source sequence(s)
    AF318404
    UniProtKB/TrEMBL
    Q8UV83, Q90Z83
    Conserved Domains (3) summary
    smart00410
    Location:29 → 127
    IG_like; Immunoglobulin like
    pfam07686
    Location:144 → 246
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:24 → 134
    Ig; Immunoglobulin domain

  4. NM_131657.1 → NP_571732.1  novel immune-type receptor 4a isoform 4 precursor

    See identical proteins and their annotated locations for NP_571732.1

    Status: PROVISIONAL

    Description
    Transcript Variant: This variant (4, also known as nitr4a-4 allele) differs in the 3' UTR and contains an alternate in-frame splice site in the 5' coding region compared to variant 6. The encoded isoform (4) is shorter than isoform 6. Variants 4 and 5 encode isoforms of the same length that differ in their amino acid composition.
    Source sequence(s)
    AF318405
    UniProtKB/TrEMBL
    Q8UV83, Q90Z82
    Conserved Domains (3) summary
    smart00410
    Location:29 → 127
    IG_like; Immunoglobulin like
    pfam07686
    Location:128 → 227
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:24 → 134
    Ig; Immunoglobulin domain

  5. NM_131658.1 → NP_571733.1  novel immune-type receptor 4a isoform 5 precursor

    See identical proteins and their annotated locations for NP_571733.1

    Status: PROVISIONAL

    Description
    Transcript Variant: This variant (5, also known as nitr4a-5 allele) differs in the 3' UTR and contains an alternate in-frame splice site in the 5' coding region compared to variant 6. The encoded isoform (5) is shorter than isoform 6. Variants 4 and 5 encode isoforms of the same length that differ in their amino acid composition.
    Source sequence(s)
    AF318406
    UniProtKB/TrEMBL
    Q8UV83, Q90Z81
    Conserved Domains (3) summary
    smart00410
    Location:29 → 127
    IG_like; Immunoglobulin like
    pfam07686
    Location:128 → 227
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:24 → 134
    Ig; Immunoglobulin domain

  6. NM_198344.3 → NP_938158.3  novel immune-type receptor 4a isoform 6 precursor

    Status: PROVISIONAL

    Description
    Transcript Variant: This variant (6) represents the longest transcript and encodes isoform 6. Variants 1, 2, 3 and 6 encode isoforms of the same length that differ in their amino acid composition.
    Source sequence(s)
    CU672228
    UniProtKB/TrEMBL
    Q8UV83
    Related
    ENSDARP00000111461.2, ENSDART00000131164.3
    Conserved Domains (1) summary
    cl11960
    Location:24 → 134
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007118.7 Reference GRCz11 Primary Assembly

    Range
    17578061..17582292 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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