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RTBDN retbindin [ Homo sapiens (human) ]

Gene ID: 83546, updated on 27-Nov-2024

Summary

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Official Symbol
RTBDNprovided by HGNC
Official Full Name
retbindinprovided by HGNC
Primary source
HGNC:HGNC:30310
See related
Ensembl:ENSG00000132026 MIM:609553; AllianceGenome:HGNC:30310
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
Summary
This gene was first identified in a study of human eye tissues. The protein encoded by this gene is preferentially expressed in the retina and may play a role in binding retinoids and other carotenoids as it shares homology with riboflavin binding proteins. Alternative splicing results in multiple transcript variants and protein isoforms. [provided by RefSeq, Jul 2012]
Expression
Biased expression in brain (RPKM 1.6), adrenal (RPKM 0.5) and 2 other tissues See more
Orthologs
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Genomic context

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See RTBDN in Genome Data Viewer
Location:
19p13.13
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12825482..12835428, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (12949999..12959945, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (12936296..12946242, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CRISPRi-FlowFISH-validated RNASEH2A regulatory element Neighboring gene CRISPRi-FlowFISH-validated PRDX2 regulatory element 4 Neighboring gene thrombospondin type 1 domain containing 8 Neighboring gene ribonuclease H2 subunit A Neighboring gene CRISPRi-FlowFISH-validated PRDX2 regulatory element 5 Neighboring gene uncharacterized LOC105372281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12940863-12941364 Neighboring gene CRISPRi-FlowFISH-validated PRDX2 regulatory element 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12945351-12945880 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:12948942-12949125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14087 Neighboring gene microtubule associated serine/threonine kinase 1 Neighboring gene CRISPRi-FlowFISH-validated KLF1 and PRDX2 regulatory element Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:12963003-12963503 Neighboring gene microRNA 6794 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:12975591-12976379 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:12976380-12977167 Neighboring gene Sharpr-MPRA regulatory region 6054 Neighboring gene CRISPRi-FlowFISH-validated KLF1 regulatory element 1 Neighboring gene deoxyribonuclease 2, lysosomal

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. Retbindin Is Capable of Protecting Photoreceptors from Flavin-Sensitized Light-Mediated Cell Death In Vitro. Kelley RA, et al. Adv Exp Med Biol, 2018. PMID 29721980
  2. Retbindin is an extracellular riboflavin-binding protein found at the photoreceptor/retinal pigment epithelium interface. Kelley RA, et al. J Biol Chem, 2015 Feb 20. PMID 25542898, Free PMC Article
  3. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. Ganesh SK, et al. Nat Genet, 2009 Nov. PMID 19862010, Free PMC Article
  4. Expressed sequence tag analysis of human retina for the NEIBank Project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. Wistow G, et al. Mol Vis, 2002 Jun 15. PMID 12107411
  5. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. Oshikawa M, et al. Invest Ophthalmol Vis Sci, 2011 Aug 22. PMID 21697133

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

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

EBI GWAS Catalog

Description
Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
EBI GWAS Catalog

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

Clone Names

  • FLJ36353

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables riboflavin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables riboflavin transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in riboflavin transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in interphotoreceptor matrix IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
retbindin

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_001080997.3 → NP_001074466.1  retbindin isoform 1 precursor

    See identical proteins and their annotated locations for NP_001074466.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform (1). Variants 1, 6 and 7 encode the same isoform.
    Source sequence(s)
    AC020934, AY028917, BM708463, BU689643
    Consensus CDS
    CCDS45994.1
    UniProtKB/Swiss-Prot
    F1T0I8, Q9BSG5, Q9BWT5
    UniProtKB/TrEMBL
    K7EIS2
    Related
    ENSP00000416375.1, ENST00000458671.6
    Conserved Domains (1) summary
    pfam03024
    Location:29 → 183
    Folate_rec; Folate receptor family

  2. NM_001270440.2 → NP_001257369.1  retbindin isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the UTRs and coding region, compared to variant 1. These differences cause translation initiation at an alternate start codon and result in an isoform (3) that is shorter and has distinct N- and C-termini, compared to isoform 1.
    Source sequence(s)
    AK093672, BU689643, CB140693
    Consensus CDS
    CCDS59356.1
    UniProtKB/TrEMBL
    K7ESG0
    Related
    ENSP00000468697.1, ENST00000589272.5
    Conserved Domains (2) summary
    pfam03024
    Location:61 → 186
    Folate_rec; Folate receptor family
    pfam13900
    Location:186 → 205
    GVQW; Putative domain of unknown function

  3. NM_001270441.2 → NP_001257370.2  retbindin isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 4, 6 and 7 encode the same isoform (1).
    Source sequence(s)
    AC020934
    Consensus CDS
    CCDS45994.1
    UniProtKB/Swiss-Prot
    F1T0I8, Q9BSG5, Q9BWT5
    UniProtKB/TrEMBL
    K7EIS2
    Related
    ENSP00000501410.1, ENST00000674343.2
    Conserved Domains (1) summary
    pfam03024
    Location:29 → 183
    Folate_rec; Folate receptor family

  4. NM_001270442.2 → NP_001257371.1  retbindin isoform 5 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (5) has a distinct N-terminus and is longer than isoform 1.
    Source sequence(s)
    AB593122, AC020934, BG471112, BU689643
    UniProtKB/TrEMBL
    K7EIS2
    Conserved Domains (1) summary
    pfam03024
    Location:35 → 189
    Folate_rec; Folate receptor family

  5. NM_001270443.2 → NP_001257372.1  retbindin isoform 1 precursor

    See identical proteins and their annotated locations for NP_001257372.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1. Variants 1, 6 and 7 encode the same isoform (1).
    Source sequence(s)
    AC020934, BM688127, BU689643, EL946853
    Consensus CDS
    CCDS45994.1
    UniProtKB/Swiss-Prot
    F1T0I8, Q9BSG5, Q9BWT5
    UniProtKB/TrEMBL
    K7EIS2
    Related
    ENSP00000376925.3, ENST00000393233.6
    Conserved Domains (1) summary
    pfam03024
    Location:29 → 183
    Folate_rec; Folate receptor family

  6. NM_001270444.2 → NP_001257373.1  retbindin isoform 1 precursor

    See identical proteins and their annotated locations for NP_001257373.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR, compared to variant 1. Variants 1, 6 and 7 encode the same isoform (1).
    Source sequence(s)
    AB593122, AC020934, BM688006, BU689643, EL946853
    Consensus CDS
    CCDS45994.1
    UniProtKB/Swiss-Prot
    F1T0I8, Q9BSG5, Q9BWT5
    UniProtKB/TrEMBL
    K7EIS2
    Related
    ENSP00000464869.1, ENST00000586969.5
    Conserved Domains (1) summary
    pfam03024
    Location:29 → 183
    Folate_rec; Folate receptor family

  7. NM_001270445.2 → NP_001257374.1  retbindin isoform 6 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR and uses an alternate in-frame splice site in the coding region, compared to variant 1. The encoded isoform (6) is shorter than isoform 1.
    Source sequence(s)
    AB593122, AC020934, BQ639040, BU689643, EL946853
    UniProtKB/TrEMBL
    K7EIS2
    Related
    ENSP00000466382.1, ENST00000589681.5
    Conserved Domains (1) summary
    pfam03024
    Location:29 → 177
    Folate_rec; Folate receptor family

  8. NM_031429.3 → NP_113617.1  retbindin isoform 2

    See identical proteins and their annotated locations for NP_113617.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is longer than isoform 1.
    Source sequence(s)
    BC005063, DB106146
    Consensus CDS
    CCDS12283.1
    UniProtKB/TrEMBL
    K7EIS2
    Related
    ENSP00000326253.4, ENST00000322912.9
    Conserved Domains (1) summary
    pfam03024
    Location:61 → 215
    Folate_rec; Folate receptor family

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    12825482..12835428 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    12949999..12959945 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BSG5.2 GenPept UniProtKB/Swiss-Prot:Q9BSG5

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