RetrogeneDB ID:

retro_ptro_2481

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:128693485..128693815(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CNIH4
Ensembl ID:ENSPTRG00000002025
Aliases:None
Description:cornichon homolog 4 (Drosophila) [Source:HGNC Symbol;Acc:25013]


Retrocopy-Parental alignment summary:






>retro_ptro_2481
GAGGACATGGTCTTTGTCTTCTTTCTCCTCAGTTGCAGGCTCATTTTTCTCTCACTCTTCATAATTACACTGTCTGATTT
AGAGTGTGATTACATTAATGCTAGATCATGTTGCTCAAAATTAAACAAGTGGGTAATTTCCAAGATTGATTGGCCATACT
ATTGTCACTGTATTCTGCACATTTTGTTGCACTGGTTCATCTTCCTTCTCAACTTACCTCTTGCCACTTGGAATATATAT
TGATTCATTATGGTGCCAAGCAGTAACATAGGAGTGTTTGATCCAACAGAAATACACAATCAAGGACAGCAAAAGTAACA
CATGAAAGAC

ORF - retro_ptro_2481 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.95 %
Parental protein coverage: 80.58 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalEAVVFVLSLLDCCALIFLSVYFIITLSDLECDYINARSCCSKLNKWVI-PELIGHTIVTV-LLLISLHWF
E..VFV..LL.C..LIFLS..FIITLSDLECDYINARSCCSKLNKWVI.P.LIGHTIVTV..L.I.LHWF
RetrocopyEDMVFVFFLLSC-RLIFLSL-FIITLSDLECDYINARSCCSKLNKWVI>PRLIGHTIVTV<ILHILLHWF
ParentalIFLLNLPVATWNIYRYIMVPSGNMGVFDPTEIHNRGQLKSHMKE
IFLLNLP.ATWNIY..IMVPS.N.GVFDPTEIHN.GQ.K.HMK.
RetrocopyIFLLNLPLATWNIY*FIMVPSSNIGVFDPTEIHNQGQQK*HMKD

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 0 .14 RPM 5 .15 RPM
SRP007412_cerebellum 0 .00 RPM 10 .40 RPM
SRP007412_heart 0 .03 RPM 10 .96 RPM
SRP007412_kidney 0 .00 RPM 17 .89 RPM
SRP007412_liver 0 .00 RPM 17 .77 RPM
SRP007412_testis 0 .11 RPM 16 .33 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2481 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2481 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2481 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3656
Pongo abelii retro_pabe_3003
Macaca mulatta retro_mmul_1796

Parental genes homology:
Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000065441 retrocopy
Callithrix jacchus ENSCJAG000000080131 retrocopy
Cavia porcellus ENSCPOG000000073101 retrocopy
Dasypus novemcinctus ENSDNOG000000070931 retrocopy
Homo sapiens ENSG000001437711 retrocopy
Gorilla gorilla ENSGGOG000000057081 retrocopy
Myotis lucifugus ENSMLUG000000031341 retrocopy
Macaca mulatta ENSMMUG000000099361 retrocopy
Nomascus leucogenys ENSNLEG000000135491 retrocopy
Ochotona princeps ENSOPRG000000015891 retrocopy
Pongo abelii ENSPPYG000000001831 retrocopy
Pan troglodytes ENSPTRG00000002025 1 retrocopy
retro_ptro_2481 ,
Pteropus vampyrus ENSPVAG000000140341 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000273962 retrocopies
Vicugna pacos ENSVPAG000000125212 retrocopies



Copyright © RetrogeneDB 2014-2017