Rtbdn (retbindin) - Rat Genome Database
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Gene: Rtbdn (retbindin) Mus musculus
Analyze
Symbol: Rtbdn
Name: retbindin
RGD ID: 1318363
MGI Page MGI
Description: Exhibits riboflavin binding activity. Localizes to extrinsic component of plasma membrane and interphotoreceptor matrix. Is expressed in central nervous system; liver; retina inner nuclear layer; retina nuclear layer; and retina outer nuclear layer. Orthologous to human RTBDN (retbindin); INTERACTS WITH choline; folic acid; L-methionine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: A330096I21Rik; BC022744; MGC31644; MGC38683; MGC38855; Rtbnd
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,672,880 - 85,683,235 (+)NCBIGRCm39mm39
GRCm38884,946,991 - 84,956,606 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,946,991 - 84,956,603 (+)EnsemblGRCm38mm10GRCm38
MGSCv37887,470,890 - 87,480,502 (+)NCBIGRCm37mm9NCBIm37
MGSCv36887,837,096 - 87,846,708 (+)NCBImm8
Celera889,247,241 - 89,256,894 (+)NCBICelera
Cytogenetic Map8C3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Ependymomas  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12477932   PMID:14610273   PMID:15226823   PMID:15489334   PMID:16141072   PMID:16141073   PMID:21677750  
PMID:21873635   PMID:25542898   PMID:26427470   PMID:29079576   PMID:32290105  


Genomics

Comparative Map Data
Rtbdn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,672,880 - 85,683,235 (+)NCBIGRCm39mm39
GRCm38884,946,991 - 84,956,606 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,946,991 - 84,956,603 (+)EnsemblGRCm38mm10GRCm38
MGSCv37887,470,890 - 87,480,502 (+)NCBIGRCm37mm9NCBIm37
MGSCv36887,837,096 - 87,846,708 (+)NCBImm8
Celera889,247,241 - 89,256,894 (+)NCBICelera
Cytogenetic Map8C3NCBI
RTBDN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1912,825,478 - 12,835,428 (-)EnsemblGRCh38hg38GRCh38
GRCh381912,825,482 - 12,835,428 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371912,936,291 - 12,946,242 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361912,797,296 - 12,807,230 (-)NCBINCBI36hg18NCBI36
Celera1912,826,003 - 12,835,935 (-)NCBI
Cytogenetic Map19p13.13NCBI
HuRef1912,507,931 - 12,517,838 (-)NCBIHuRef
CHM1_11912,936,788 - 12,946,749 (-)NCBICHM1_1
Rtbdn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01926,065,784 - 26,073,194 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1926,066,127 - 26,073,194 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01937,041,750 - 37,048,817 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41924,853,294 - 24,860,541 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11924,858,403 - 24,865,634 (-)NCBI
Celera1922,754,995 - 22,761,858 (-)NCBICelera
Cytogenetic Map19q11NCBI
Rtbdn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541531,895,507 - 31,899,303 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541531,895,446 - 31,899,927 (-)NCBIChiLan1.0ChiLan1.0
RTBDN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11913,129,659 - 13,139,842 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1913,129,659 - 13,139,842 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01912,387,165 - 12,397,157 (-)NCBIMhudiblu_PPA_v0panPan3
RTBDN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2049,334,127 - 49,337,223 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12049,324,843 - 49,337,226 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Rtbdn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366591,907,933 - 1,911,690 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTBDN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl266,188,089 - 66,193,654 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1266,188,077 - 66,191,434 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2266,529,481 - 66,546,422 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RTBDN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1611,508,417 - 11,524,011 (-)NCBI
Rtbdn
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624901421,624 - 426,655 (-)NCBI

Position Markers
UniSTS:225333  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38884,948,692 - 84,948,803UniSTSGRCm38
MGSCv37887,472,591 - 87,472,702UniSTSGRCm37
Celera889,248,940 - 89,249,051UniSTS
Cytogenetic Map8C3UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4140967Bmd39_mbone mineral density 39 (mouse)Not determined832016544117238700Mouse
1558875Eae31_mexperimental allergic encephalomyelitis susceptibility 31 (mouse)Not determined834642776114837007Mouse
1301013Capsq4_mcapsaicin sensitivity related QTL 4 (mouse)Not determined83616300092728652Mouse
27226754Femd6_mfemur midshaft diameter 6, 10 week (mouse)837400000109600000Mouse
12904744Carcdq1_mcardiac collagen deposition QTL 1 (mouse)83970925694689598Mouse
14700686Civq3_mcerebral infarct volume QTL 3 (mouse)85188219185882191Mouse
1301506Aevm1_mautoimmune extremity vasculitis in MRL mice 1 (mouse)Not determined85428781788287993Mouse
1301952Im3_mimmunoregulatory 3 (mouse)Not determined85470661488706763Mouse
10412287Carg3_mCandida albicans resistance gene 3 (mouse)Not determined85554502889545028Mouse
11353828Gf7_mgonadal fat pad weight 7 (mouse)85820147992201479Mouse
10043975Obq31_mobesity QTL 31 (mouse)Not determined85840977692409776Mouse
1301688Orch6_mautoimmune orchitis resistance 6 (mouse)Not determined86078685094786976Mouse
4141285Tgq18_mtriglyceride QTL 18 (mouse)Not determined6346010797460107Mouse
4141797Skmw16_mskeletal muscle weight 16 (mouse)Not determined86393954797939696Mouse
1357787Vtbt5_mvertebral trabecular bone trait 5 (mouse)Not determined86535776899357920Mouse
10043992Hbnr11_mHeligmosomoides bakeri nematode resistance 11 (mouse)Not determined86560020799600347Mouse
1301767Fcsa2_mfemoral cross-sectional area 2 (mouse)Not determined870305375104305495Mouse
4142283Imraq2_mimmune response to AAV2 QTL 2 (mouse)Not determined870305375104305495Mouse
1558780Idd22_minsulin dependent diabetes susceptibility 22 (mouse)Not determined871102903105103009Mouse
4141395Char2a_mP. chabaudi malaria resistance QTL 2a (mouse)Not determined7113678390202598Mouse
4142023W3q5_mweight 3 weeks QTL 5 (mouse)Not determined71287817123895615Mouse
1357708Orq1_movulation rate QTL 1 (mouse)Not determined871287817123895615Mouse
1301872Cd4ts3_mCD4 T cell subset 3 (mouse)Not determined871396181105396393Mouse
1300920Pitm3_mprion incubation time 3 (mouse)Not determined873202495107202598Mouse
27095912Pglq14_mpelvic girdle length QTL 14, 16 week (mouse)873400000126100000Mouse
1558890Lith18_mlithogenic gene 18 (mouse)Not determined875675517109675623Mouse
1357470Obq16_mobesity QTL 16 (mouse)Not determined875685348109685497Mouse
1301808Nhdlq1_mnon-HDL QTL 1 (mouse)Not determined875685348109685497Mouse
1301874Hdlq16_mHDL QTL 16 (mouse)Not determined875685348109685497Mouse
10412234Nhdlq14_mnon-HDL QTL 14 (mouse)Not determined875685348109685497Mouse
1301099Cbm2_mcerebellum weight 2 (mouse)Not determined878518613112518703Mouse
1301581Char2_mP. chabaudi malaria resistance QTL 2 (mouse)Not determined879082178113082403Mouse
12904012Cfq10_mconditioned fear QTL 10 (mouse)88006677589014359Mouse
10755530Wbc2_mwhite blood cell count 2 (mouse)881092664115092664Mouse
10755519Wbc1_mwhite blood cell count 1 (mouse)881619151115619151Mouse
1301766Desp1_mdespair 1 (mouse)Not determined884759576118759741Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:760
Count of miRNA genes:189
Interacting mature miRNAs:201
Transcripts:ENSMUST00000067472, ENSMUST00000109740, ENSMUST00000121880, ENSMUST00000152378
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001357326 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001357328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_144929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036153960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC161765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC163703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK039726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK080715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY428631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY527275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY527276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC022744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC023051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC024753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC027079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CD742502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000067472   ⟹   ENSMUSP00000070558
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl884,946,991 - 84,956,603 (+)Ensembl
RefSeq Acc Id: ENSMUST00000109740   ⟹   ENSMUSP00000105362
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl884,946,991 - 84,956,603 (+)Ensembl
RefSeq Acc Id: ENSMUST00000121880   ⟹   ENSMUSP00000113982
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl884,949,860 - 84,956,603 (+)Ensembl
RefSeq Acc Id: ENSMUST00000152378   ⟹   ENSMUSP00000132841
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl884,951,181 - 84,956,511 (+)Ensembl
RefSeq Acc Id: NM_001357326   ⟹   NP_001344255
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39885,673,620 - 85,683,235 (+)NCBI
GRCm38884,946,991 - 84,956,606 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001357328   ⟹   NP_001344257
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39885,674,619 - 85,683,235 (+)NCBI
GRCm38884,947,990 - 84,956,606 (+)NCBI
Sequence:
RefSeq Acc Id: NM_144929   ⟹   NP_659178
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39885,673,620 - 85,683,235 (+)NCBI
GRCm38884,946,991 - 84,956,606 (+)NCBI
MGSCv37887,470,890 - 87,480,502 (+)RGD
Celera889,247,241 - 89,256,894 (+)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_036153960   ⟹   XP_036009853
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39885,672,880 - 85,683,235 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_659178   ⟸   NM_144929
- Peptide Label: precursor
- UniProtKB: Q8QZY4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001344255   ⟸   NM_001357326
- Peptide Label: precursor
RefSeq Acc Id: NP_001344257   ⟸   NM_001357328
- Peptide Label: precursor
RefSeq Acc Id: ENSMUSP00000132841   ⟸   ENSMUST00000152378
RefSeq Acc Id: ENSMUSP00000070558   ⟸   ENSMUST00000067472
RefSeq Acc Id: ENSMUSP00000105362   ⟸   ENSMUST00000109740
RefSeq Acc Id: ENSMUSP00000113982   ⟸   ENSMUST00000121880
RefSeq Acc Id: XP_036009853   ⟸   XM_036153960
- Peptide Label: isoform X1
Protein Domains
Folate_rec

Promoters
RGD ID:8667715
Promoter ID:EPDNEW_M11889
Type:initiation region
Name:Rtbdn_1
Description:Mus musculus retbindin , transcript variant 3, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M11890  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38884,946,993 - 84,947,053EPDNEW
RGD ID:8667717
Promoter ID:EPDNEW_M11890
Type:initiation region
Name:Rtbdn_2
Description:Mus musculus retbindin , transcript variant 3, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M11889  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38884,949,939 - 84,949,999EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2443686 AgrOrtholog
Ensembl Genes ENSMUSG00000048617 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000070558 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000105362 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000113982 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000132841 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000067472 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000109740 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000121880 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000152378 UniProtKB/TrEMBL
InterPro Folate_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Folate_rcpt-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:234542 UniProtKB/Swiss-Prot
MGD MGI:2443686 ENTREZGENE
NCBI Gene 234542 ENTREZGENE
PANTHER PTHR10517 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Folate_rec UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rtbdn PhenoGen
UniGene Mm.461701 ENTREZGENE
UniProt E9PXB4_MOUSE UniProtKB/TrEMBL
  Q8QZY4 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6T898 UniProtKB/Swiss-Prot