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    RTBDN retbindin [ Homo sapiens (human) ]

    Gene ID: 83546, updated on 10-Dec-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
    mouse all
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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: 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. 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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    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

    Gene LinkOut

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

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