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Aliases for RTBDN Gene

Aliases for RTBDN Gene

External Ids for RTBDN Gene

Previous GeneCards Identifiers for RTBDN Gene

  • GC19M013067
  • GC19M013159
  • GC19M012781
  • GC19M012936
  • GC19M012507

Summaries for RTBDN Gene

Entrez Gene Summary for RTBDN Gene

  • 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]

GeneCards Summary for RTBDN Gene

RTBDN (Retbindin) is a Protein Coding gene.

UniProtKB/Swiss-Prot for RTBDN Gene

  • Riboflavin-binding protein which might have a role in retinal flavin transport.

Additional gene information for RTBDN Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RTBDN Gene

Genomics for RTBDN Gene

GeneHancer (GH) Regulatory Elements for RTBDN Gene

Promoters and enhancers for RTBDN Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I012835 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE 550.8 +2.2 2223 1.5 PKNOX1 FOXA2 ARNT ARID4B NEUROD1 SIN3A ZNF2 E2F8 SP3 SP5 RTBDN DNASE2 GCDH MAST1 HOOK2
GH19I012838 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 -0.2 -197 0.3 RB1 ZNF335 EGR1 ZNF143 RCOR1 CREM EGR2 SMARCA5 REST ZNF398 MAST1 RTBDN GC19M012844 HOOK2
GH19I012833 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 +4.0 4010 1 HDAC1 HDGF RB1 KLF17 NFXL1 ZNF335 GLIS2 EGR1 ATF7 EGR2 MAST1 RTBDN HOOK2
GH19I012830 Promoter/Enhancer 1.2 EPDnew ENCODE 550.4 +7.6 7599 0.1 ZNF639 TFAP4 SAP130 DACH1 SP2 NCOA1 REST SP1 ZFHX2 EGR1 RTBDN GC19M012828 LOC105372281 MAST1 HOOK2
GH19I012839 Enhancer 0.7 ENCODE 550.8 -1.0 -1005 0.1 SCRT1 HDGF MXI1 ATF1 L3MBTL2 ZBTB21 CEBPB ZNF398 MNT ATF2 RTBDN GC19M012844 MAST1 HOOK2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RTBDN on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RTBDN gene promoter:

Genomic Locations for RTBDN Gene

Genomic Locations for RTBDN Gene
chr19:12,825,477-12,838,267
(GRCh38/hg38)
Size:
12,791 bases
Orientation:
Minus strand
chr19:12,936,292-12,946,242
(GRCh37/hg19)

Genomic View for RTBDN Gene

Genes around RTBDN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTBDN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTBDN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTBDN Gene

Proteins for RTBDN Gene

  • Protein details for RTBDN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BSG5-RTBDN_HUMAN
    Recommended name:
    Retbindin
    Protein Accession:
    Q9BSG5
    Secondary Accessions:
    • F1T0I8
    • Q9BWT5

    Protein attributes for RTBDN Gene

    Size:
    229 amino acids
    Molecular mass:
    24615 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for RTBDN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RTBDN Gene

Post-translational modifications for RTBDN Gene

No data available for DME Specific Peptides for RTBDN Gene

Domains & Families for RTBDN Gene

Gene Families for RTBDN Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for RTBDN Gene

Suggested Antigen Peptide Sequences for RTBDN Gene

Graphical View of Domain Structure for InterPro Entry

Q9BSG5

UniProtKB/Swiss-Prot:

RTBDN_HUMAN :
  • Belongs to the folate receptor family.
Family:
  • Belongs to the folate receptor family.
genes like me logo Genes that share domains with RTBDN: view

Function for RTBDN Gene

Molecular function for RTBDN Gene

UniProtKB/Swiss-Prot Function:
Riboflavin-binding protein which might have a role in retinal flavin transport.

Phenotypes From GWAS Catalog for RTBDN Gene

genes like me logo Genes that share phenotypes with RTBDN: view

Animal Models for RTBDN Gene

MGI Knock Outs for RTBDN:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RTBDN Gene

Localization for RTBDN Gene

Subcellular locations from UniProtKB/Swiss-Prot for RTBDN Gene

Secreted, extracellular space, extracellular matrix, interphotoreceptor matrix. Cell membrane; Peripheral membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RTBDN gene
Compartment Confidence
plasma membrane 4
extracellular 3
nucleus 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RTBDN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0033165 interphotoreceptor matrix IEA --
genes like me logo Genes that share ontologies with RTBDN: view

Pathways & Interactions for RTBDN Gene

SuperPathways for RTBDN Gene

No Data Available

Gene Ontology (GO) - Biological Process for RTBDN Gene

None

No data available for Pathways by source and SIGNOR curated interactions for RTBDN Gene

Drugs & Compounds for RTBDN Gene

No Compound Related Data Available

Transcripts for RTBDN Gene

Unigene Clusters for RTBDN Gene

Retbindin:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RTBDN Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11a · 11b · 11c · 11d · 11e
SP1: - - - - - -
SP2: - - - - - - -
SP3: - - - - - -
SP4: - - - - - - -
SP5: - - - - -
SP6: - - - -
SP7: - -
SP8: - - - - - - -
SP9: - - - - -
SP10: - -
SP11: - - - - - - -
SP12: - -

Relevant External Links for RTBDN Gene

GeneLoc Exon Structure for
RTBDN
ECgene alternative splicing isoforms for
RTBDN

Expression for RTBDN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RTBDN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RTBDN Gene

This gene is overexpressed in Pituitary (x11.1), Brain - Amygdala (x6.2), Brain - Frontal Cortex (BA9) (x5.9), Brain - Cortex (x5.9), Brain - Anterior cingulate cortex (BA24) (x5.7), and Brain - Hippocampus (x4.6).

Protein differential expression in normal tissues from HIPED for RTBDN Gene

This gene is overexpressed in Vitreous humor (66.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RTBDN Gene



Protein tissue co-expression partners for RTBDN Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RTBDN Gene:

RTBDN

SOURCE GeneReport for Unigene cluster for RTBDN Gene:

Hs.21162

mRNA Expression by UniProt/SwissProt for RTBDN Gene:

Q9BSG5-RTBDN_HUMAN
Tissue specificity: Expressed in peripheral retina (at protein level).

Evidence on tissue expression from TISSUES for RTBDN Gene

  • Eye(4.7)
  • Muscle(2.6)
  • Heart(2.5)
  • Kidney(2.3)
  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with RTBDN: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RTBDN Gene

Orthologs for RTBDN Gene

This gene was present in the common ancestor of mammals.

Orthologs for RTBDN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RTBDN 33 34
  • 99.36 (n)
dog
(Canis familiaris)
Mammalia RTBDN 33 34
  • 79.05 (n)
cow
(Bos Taurus)
Mammalia RTBDN 33 34
  • 76.62 (n)
rat
(Rattus norvegicus)
Mammalia Rtbdn 33
  • 73.77 (n)
mouse
(Mus musculus)
Mammalia Rtbdn 33 16 34
  • 73.03 (n)
Species where no ortholog for RTBDN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for RTBDN Gene

ENSEMBL:
Gene Tree for RTBDN (if available)
TreeFam:
Gene Tree for RTBDN (if available)

Paralogs for RTBDN Gene

No data available for Paralogs for RTBDN Gene

Variants for RTBDN Gene

Sequence variations from dbSNP and Humsavar for RTBDN Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000163967 -- 12,837,150(-) T/A upstream_transcript_variant
rs1000568610 -- 12,830,590(-) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000667526 -- 12,830,942(-) TGTGTGTGTGT/TGTGTGTGTGTGT genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1001122229 -- 12,831,213(-) T/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1001158221 -- 12,837,125(-) G/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RTBDN Gene

Variant ID Type Subtype PubMed ID
nsv953977 CNV deletion 24416366
nsv2420 CNV insertion 18451855

Variation tolerance for RTBDN Gene

Residual Variation Intolerance Score: 72.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.35; 53.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RTBDN Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTBDN

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTBDN Gene

Disorders for RTBDN Gene

Additional Disease Information for RTBDN

No disorders were found for RTBDN Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RTBDN Gene

Publications for RTBDN Gene

  1. 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. (PMID: 12107411) Wistow G … Peterson K (Molecular vision 2002) 2 3 4 58
  2. Retbindin is an extracellular riboflavin-binding protein found at the photoreceptor/retinal pigment epithelium interface. (PMID: 25542898) Kelley RA … Naash MI (The Journal of biological chemistry 2015) 3 4 58
  3. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. (PMID: 21697133) Oshikawa M … Kato S (Investigative ophthalmology & visual science 2011) 3 4 58
  4. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. (PMID: 19862010) Ganesh SK … Lin JP (Nature genetics 2009) 3 44 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for RTBDN Gene

Sources for RTBDN Gene

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