RetrogeneDB ID:

retro_ptro_1393

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:20:21620479..21620874(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GSTM3
Ensembl ID:ENSPTRG00000001063
Aliases:None
Description:Pan troglodytes glutathione S-transferase mu 3 (brain) (GSTM3), mRNA. [Source:RefSeq mRNA;Acc:NM_001246568]


Retrocopy-Parental alignment summary:






>retro_ptro_1393
GGTGAGACTGAAGAAGGAAAGGTGCCAGGAGACATCAGGGAGGACCAAATGGTGGAATACCACCTGCAGCTGAAACAGCT
CCACCATGACCCTGACATGAAACATGGAAGCCTCCATACTCGGAACTGCAACCTGGGCAGCTGAAACATTTCTCCTTGTT
TCTGAGGAAGTCATGGTTTCCAGGGGGAAAGCTCACCTTTTTGGATATTCTTACCTGTGATGTCTTAGATCAGAACTGTA
TGTTTGAGCTCAAGTGCCTGTATGAGTTCCCAAATCTGAGGACTTCATGCATCACATTGCAGCTTTGGAGGAAAGAGCTG
CCCCTGTGCAATCTGCCTGTTCTTCGGGATGCCAGTCAGCAGCGAGATGGCCCAGTGGGGACCAAGAGCGTATGC

ORF - retro_ptro_1393 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.07 %
Parental protein coverage: 59.56 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalGETEEEKIRVDIIENQVMDFRTQLIRLCYSSD-HEKLKPQYLEELPGQLKQFSMFLGKFSWFAGEKLTFV
GETEE.K...DI.E.Q......QL..L....D.HE..KP.Y.E..PGQLK.FS.FL.K.SWF.G.KLTF.
RetrocopyGETEEGKVPGDIREDQMVEYHLQLKQLHHDPD<HETWKPPYSELQPGQLKHFSLFLRK-SWFPGGKLTFL
ParentalDFLTYDILDQNRIFDPKCLDEFPNLKA-FMCRFEALEKIAAYLQSD-QFFKMPINNKMAQW-GNKPVC
D.LT.D.LDQN..F..KCL.EFPNL...FM....ALE..AA..QS...FF.MP....MAQW.G.K.VC
RetrocopyDILTCDVLDQNCMFELKCLYEFPNLRT<FMHHIAALEERAAPVQSA<LFFGMPVSSEMAQW<GTKSVC

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 1 .57 RPM 16 .50 RPM
SRP007412_cerebellum 0 .43 RPM 7 .21 RPM
SRP007412_heart 0 .00 RPM 1 .78 RPM
SRP007412_kidney 0 .00 RPM 87 .74 RPM
SRP007412_liver 0 .00 RPM 0 .69 RPM
SRP007412_testis 0 .00 RPM 1080 .92 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1393 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1393 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1393 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_610

Parental genes homology:
Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000053802 retrocopies
Callithrix jacchus ENSCJAG000000031681 retrocopy
Erinaceus europaeus ENSEEUG000000142111 retrocopy
Echinops telfairi ENSETEG000000058172 retrocopies
Homo sapiens ENSG000001342021 retrocopy
Microcebus murinus ENSMICG000000051851 retrocopy
Macaca mulatta ENSMMUG000000080292 retrocopies
Monodelphis domestica ENSMODG000000018991 retrocopy
Mus musculus ENSMUSG000000040322 retrocopies
Nomascus leucogenys ENSNLEG000000033021 retrocopy
Pan troglodytes ENSPTRG000000010612 retrocopies
Pan troglodytes ENSPTRG00000001063 2 retrocopies
retro_ptro_1393 , retro_ptro_1709,
Rattus norvegicus ENSRNOG000000470341 retrocopy
Sus scrofa ENSSSCG000000068212 retrocopies
Tarsius syrichta ENSTSYG000000067361 retrocopy
Tursiops truncatus ENSTTRG000000096821 retrocopy



Copyright © RetrogeneDB 2014-2017