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
Data last updated at UCSC: 2013-06-14
Sequence and Links to Tools and Databases
Primer design for this transcript
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: Cholesterol, HDL , , .
[PubMed 0 ]
Cholesterol, HDL , , .
[PubMed 0 ]
Cholesterol, HDL , , .
[PubMed 0 ]
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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
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Common Gene Haplotype Alleles
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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
Microarray Expression Data
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mRNA Secondary Structure of 3' and 5' UTRs
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
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.
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
Other Names for This Gene
Gene Model Information
category:
coding
nonsense-mediated-decay:
no
RNA accession:
NM_153828.2
exon count:
7 CDS single in 3' UTR:
no
RNA size:
2414
ORF size:
1122 CDS single in intron:
no
Alignment % ID:
100.00
txCdsPredict score:
2444.00 frame 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
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Methods, Credits, and Use Restrictions
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for details on how this gene model was made and data restrictions if any.