Human Gene RTN4 (uc002ryg.3)
  Description: Homo sapiens reticulon 4 (RTN4), transcript variant 2, mRNA.
RefSeq Summary (NM_153828): This gene belongs to the family of reticulon encoding genes. Reticulons are associated with the endoplasmic reticulum, and are involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells. The product of this gene is a potent neurite outgrowth inhibitor which may also help block the regeneration of the central nervous system in higher vertebrates. Alternatively spliced transcript variants derived both from differential splicing and differential promoter usage and encoding different isoforms have been identified. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr2:55,199,327-55,277,734 Size: 78,408 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr2:55,200,292-55,277,436 Size: 77,145 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:55,199,327-55,277,734)mRNA (may differ from genome)Protein (373 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHuman Cortex Gene ExpressionLynxMalacardsMGI
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RTN4
CDC HuGE Published Literature: RTN4
Positive Disease Associations: Cholesterol, HDL , Hypertension , Lipids , obesity (extreme) , schizophrenia , Triglycerides
Related Studies:
  1. Cholesterol, HDL
    , , . [PubMed 0]
  2. Cholesterol, HDL
    , , . [PubMed 0]
  3. Cholesterol, HDL
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: RTN4
Diseases sorted by gene-association score: demyelinating disease (3), alzheimer disease (2), pedophilia (2), disease of mental health (2), amyotrophic lateral sclerosis 1 (2), specific developmental disorder (2), schizophrenia (2), partial fetal alcohol syndrome (1), dependent personality disorder (1), paraphilia disorder (1), space motion sickness (1), separation anxiety disorder (1), ideomotor apraxia (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D001564 Benzo(a)pyrene
  • D013629 Tamoxifen
  • D013749 Tetrachlorodibenzodioxin
  • C006253 pirinixic acid
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • C023514 2,6-dinitrotoluene
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D015127 9,10-Dimethyl-1,2-benzanthracene
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 124.04 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 2836.30 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -136.60298-0.458 Picture PostScript Text
3' UTR -246.38965-0.255 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF02453 - Reticulon

ModBase Predicted Comparative 3D Structure on Q9NQC3-2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  KJ906268 - Synthetic construct Homo sapiens clone ccsbBroadEn_15938 RTN4 gene, encodes complete protein.
AF087901 - Homo sapiens reticulon 4c mRNA, complete cds.
AF177332 - Homo sapiens clone SP1507 unknown mRNA.
AF132048 - Homo sapiens foocen-s mRNA, complete cds.
JA482188 - Sequence 171 from Patent WO2011072091.
JE980480 - Sequence 171 from Patent EP2862929.
AY102276 - Homo sapiens RTN4 isoform C (RTN4) mRNA, complete cds; alternatively spliced.
AY123250 - Homo sapiens RTN4 isoform G (RTN4) mRNA, complete cds; alternatively spliced.
AY123249 - Homo sapiens RTN4 isoform F (RTN4) mRNA, complete cds; alternatively spliced.
JA482190 - Sequence 173 from Patent WO2011072091.
JE980482 - Sequence 173 from Patent EP2862929.
AY123248 - Homo sapiens RTN4 isoform E (RTN4) mRNA, complete cds; alternatively spliced.
AY123247 - Homo sapiens RTN4 isoform D (RTN4) mRNA, complete cds; alternatively spliced.
AF148537 - Homo sapiens reticulon 4a mRNA, complete cds.
AF148538 - Homo sapiens reticulon 4b mRNA, complete cds.
AF132047 - Homo sapiens foocen-m mRNA, complete cds.
AY102277 - Homo sapiens RTN4 isoform B1 (RTN4) mRNA, complete cds; alternatively spliced.
AY102278 - Homo sapiens RTN4 isoform B2 (RTN4) mRNA, complete cds; alternatively spliced.
AY102279 - Homo sapiens RTN4 isoform A (RTN4) mRNA, complete cds; alternatively spliced.
BC150182 - Homo sapiens reticulon 4, mRNA (cDNA clone MGC:164945 IMAGE:40148210), complete cds.
BC152555 - Homo sapiens reticulon 4, mRNA (cDNA clone MGC:165109 IMAGE:40148984), complete cds.
AY123246 - Homo sapiens RTN4 isoform Ab (RTN4) mRNA, complete cds; alternatively spliced.
JA482186 - Sequence 169 from Patent WO2011072091.
JA482187 - Sequence 170 from Patent WO2011072091.
JA482189 - Sequence 172 from Patent WO2011072091.
JE980478 - Sequence 169 from Patent EP2862929.
JE980479 - Sequence 170 from Patent EP2862929.
JE980481 - Sequence 172 from Patent EP2862929.
AY123245 - Homo sapiens RTN4 isoform Aa (RTN4) mRNA, complete cds; alternatively spliced.
AK172726 - Homo sapiens cDNA PSEC0023 fis, clone: NT2RP1000386.
AB015639 - Homo sapiens ASY mRNA, complete cds.
BC014366 - Homo sapiens reticulon 4, mRNA (cDNA clone IMAGE:3933041), complete cds.
AF125103 - Homo sapiens neuroendocrine specific protein c homolog mRNA, complete cds.
AF077050 - Homo sapiens neuroendocrine-specific protein C homolog mRNA, complete cds.
JD410376 - Sequence 391400 from Patent EP1572962.
JD059273 - Sequence 40297 from Patent EP1572962.
JD038323 - Sequence 19347 from Patent EP1572962.
BC131571 - Homo sapiens cDNA clone IMAGE:40108446.
BC007109 - Homo sapiens reticulon 4, mRNA (cDNA clone IMAGE:4291127), complete cds.
BC001035 - Homo sapiens reticulon 4, mRNA (cDNA clone IMAGE:3139770), complete cds.
AB073351 - Homo sapiens primary neuroblastoma mRNA for NOGO-A, partial cds, clone:Nbla00271.
BC010737 - Homo sapiens reticulon 4, mRNA (cDNA clone IMAGE:3901353), complete cds.
BC071848 - Homo sapiens reticulon 4, mRNA (cDNA clone IMAGE:4635625), complete cds.
BC152425 - Homo sapiens reticulon 4, mRNA (cDNA clone MGC:176660 IMAGE:8862539), complete cds.
BC026788 - Homo sapiens reticulon 4, mRNA (cDNA clone IMAGE:3862911), complete cds.
BC012335 - Homo sapiens cDNA clone IMAGE:3510627, **** WARNING: chimeric clone ****.
BC016165 - Homo sapiens reticulon 4, mRNA (cDNA clone IMAGE:3505850), complete cds.
BC068991 - Homo sapiens reticulon 4, mRNA (cDNA clone IMAGE:4634289), complete cds.
AF063601 - Homo sapiens brain my043 protein mRNA, complete cds.
AK130812 - Homo sapiens cDNA FLJ27302 fis, clone TMS04776.
AB020693 - Homo sapiens KIAA0886 mRNA for KIAA0886 protein.
AX195249 - Sequence 5 from Patent WO0151520.
AK129806 - Homo sapiens cDNA FLJ26295 fis, clone DMC07157.
AK075039 - Homo sapiens cDNA FLJ90558 fis, clone OVARC1001030.
AK090714 - Homo sapiens cDNA FLJ33395 fis, clone BRACE2007064.
BC012619 - Homo sapiens reticulon 4, mRNA (cDNA clone IMAGE:4082756), complete cds.
AF333336 - Homo sapiens testis specific reticulon 5 protein mRNA, complete cds.
AB040462 - Homo sapiens mRNA for RTN-xL, complete cds.
AB040463 - Homo sapiens mRNA for RTN-xS, complete cds.
JD432925 - Sequence 413949 from Patent EP1572962.
DL491385 - Novel nucleic acids.
DL490013 - Novel nucleic acids.
DQ598072 - Homo sapiens piRNA piR-36138, complete sequence.
AJ251385 - Homo sapiens mRNA for Nogo-C protein (Nogo gene).
DQ778739 - Homo sapiens Nogo-C (NOGOC) mRNA, complete cds.
AF320999 - Homo sapiens Nogo-A protein short form mRNA, complete cds, alternatively spliced.
AJ251383 - Homo sapiens mRNA for Nogo-A protein (Nogo gene).
AJ251384 - Homo sapiens mRNA for Nogo-B protein (Nogo gene).
KJ906267 - Synthetic construct Homo sapiens clone ccsbBroadEn_15937 RTN4 gene, encodes complete protein.
KJ894399 - Synthetic construct Homo sapiens clone ccsbBroadEn_03793 RTN4 gene, encodes complete protein.
KJ894400 - Synthetic construct Homo sapiens clone ccsbBroadEn_03794 RTN4 gene, encodes complete protein.
AM392753 - Synthetic construct Homo sapiens clone IMAGE:100003033 for hypothetical protein (RTN4 gene).
AM393280 - Synthetic construct Homo sapiens clone IMAGE:100003034 for hypothetical protein (RTN4 gene).
AB384033 - Synthetic construct DNA, clone: pF1KSDA0886, Homo sapiens RTN4 gene for reticulon-4, complete cds, without stop codon, in Flexi system.
AM393122 - Synthetic construct Homo sapiens clone IMAGE:100002775 for hypothetical protein (RTN4 gene).
AM393537 - Synthetic construct Homo sapiens clone IMAGE:100002776 for hypothetical protein (RTN4 gene).
BC139928 - Synthetic construct Homo sapiens clone IMAGE:100002775, MGC:165147 reticulon 4 (RTN4) mRNA, encodes complete protein.
AM393104 - Synthetic construct Homo sapiens clone IMAGE:100002769 for hypothetical protein (RTN4 gene).
AM393557 - Synthetic construct Homo sapiens clone IMAGE:100002793 for hypothetical protein (RTN4 gene).
AK093785 - Homo sapiens cDNA FLJ36466 fis, clone THYMU2015409.
CQ873854 - Sequence 273 from Patent WO2004076622.
DD413691 - Regulation of Mammalian Cells.
AK098385 - Homo sapiens cDNA FLJ25519 fis, clone CBR06737, highly similar to Homo sapiens mRNA for Nogo-A protein (Nogo gene).
CU687182 - Synthetic construct Homo sapiens gateway clone IMAGE:100023156 5' read RTN4 mRNA.
DL491540 - Novel nucleic acids.
DL490145 - Novel nucleic acids.
JD126928 - Sequence 107952 from Patent EP1572962.
JD371792 - Sequence 352816 from Patent EP1572962.
JD395086 - Sequence 376110 from Patent EP1572962.
JD099221 - Sequence 80245 from Patent EP1572962.
JD246359 - Sequence 227383 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NQC3 (Reactome details) participates in the following event(s):

R-HSA-193655 Myelin components can interact with p75NTR:NgR:LINGO1
R-HSA-9012761 The p75NTR:NgR:MDGI binds RHOA-GDI
R-HSA-193696 The p75NTR:NgR:MDGI complex reduces RHOA-GDI activity, displacing RHOA
R-HSA-193634 Axonal growth inhibition (RHOA activation)
R-HSA-193697 p75NTR regulates axonogenesis
R-HSA-193704 p75 NTR receptor-mediated signalling
R-HSA-73887 Death Receptor Signalling
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA0886, My043, NM_153828, NOGO, NP_722550, Q9NQC3-2, SP1507
UCSC ID: uc002ryg.3
RefSeq Accession: NM_153828
Protein: Q9NQC3-2, splice isoform of Q9NQC3 CCDS: CCDS1851.1, CCDS42683.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_153828.2
exon count: 7CDS single in 3' UTR: no RNA size: 2414
ORF size: 1122CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2444.00frame shift in genome: no % Coverage: 98.80
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.