RetrogeneDB ID:

retro_ptro_1268

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:18:53924129..53924609(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RSL24D1
Ensembl ID:ENSPTRG00000007094
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1268
ATGCGCATCGAGAAGTGTTATTTCTGTTCGGGGCCCATCTACCCTGGCTATGACATGATGTTCATCCACAACGATTGCAA
AGTGTTCGGATTTTGTAAATCTAAATGTCATAAACACTTTAAAAAGAAGTGCAATCCTTGCAAAGTTAGGCGGACCAAAC
CATTCCAGAAAGCAGCTGGTAAAGAGCTTACAGTAGATAATTCATTTGAATTTGACAGACATAGAAATGAACCTATCAAA
TACCAGCGAGAGCTATGGAATAGAACTATTGATGCAATGAAGAGAGTTGAAGAGATCAAACAGAAACGCCAAGCTAAATT
TATAATGAACAGATTGAAGAAAAATAAAGCGCTACAGAAAGTTCAGGATATCAAAGAAGTCAAGCAAAGCATCCATCTTA
TCCAAGCCCGTCTTGCAGGCAAAGGGAAGGAGTTGGAAGAGAAAATGGTACAGCAGTTACAACAGGATGTGGACATGAAG

ORF - retro_ptro_1268 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.25 %
Parental protein coverage: 98.16 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMRIEKCYFCSGPIYPGHGMMFVRNDCKVFRFCKSKCHKNFKKKRNPRKVRWTKAFRKAAGKELTVDNSFE
MRIEKCYFCSGPIYPG..MMF..NDCKVF.FCKSKCHK.FKKK.NP.KVR.TK.F.KAAGKELTVDNSFE
RetrocopyMRIEKCYFCSGPIYPGYDMMFIHNDCKVFGFCKSKCHKHFKKKCNPCKVRRTKPFQKAAGKELTVDNSFE
ParentalFEKRRNEPIKYQRELWNKTIDAMKRVEEIKQKRQAKFIMNRLKKNKELQKVQDIKEVKQNIHLIRAPLAG
F...RNEPIKYQRELWN.TIDAMKRVEEIKQKRQAKFIMNRLKKNK.LQKVQDIKEVKQ.IHLI.A.LAG
RetrocopyFDRHRNEPIKYQRELWNRTIDAMKRVEEIKQKRQAKFIMNRLKKNKALQKVQDIKEVKQSIHLIQARLAG
ParentalKGKQLEEKMVQQLQEDVDME
KGK.LEEKMVQQLQ.DVDM.
RetrocopyKGKELEEKMVQQLQQDVDMK

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 .00 RPM 34 .73 RPM
SRP007412_cerebellum 0 .00 RPM 47 .82 RPM
SRP007412_heart 0 .00 RPM 41 .65 RPM
SRP007412_kidney 0 .03 RPM 38 .34 RPM
SRP007412_liver 0 .00 RPM 35 .03 RPM
SRP007412_testis 0 .00 RPM 51 .22 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1268 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1268 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1268 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1887
Pongo abelii retro_pabe_1568

Parental genes homology:
Parental genes homology involve 29 parental genes, and 171 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000013421 retrocopy
Canis familiaris ENSCAFG000000159041 retrocopy
Choloepus hoffmanni ENSCHOG000000117999 retrocopies
Callithrix jacchus ENSCJAG000000007952 retrocopies
Dasypus novemcinctus ENSDNOG000000108122 retrocopies
Equus caballus ENSECAG000000188611 retrocopy
Erinaceus europaeus ENSEEUG000000067551 retrocopy
Felis catus ENSFCAG000000192721 retrocopy
Homo sapiens ENSG0000013787617 retrocopies
Gorilla gorilla ENSGGOG0000000519515 retrocopies
Microcebus murinus ENSMICG000000026213 retrocopies
Myotis lucifugus ENSMLUG000000119764 retrocopies
Macaca mulatta ENSMMUG0000002069316 retrocopies
Monodelphis domestica ENSMODG000000079661 retrocopy
Mustela putorius furoENSMPUG000000022281 retrocopy
Mus musculus ENSMUSG000000322151 retrocopy
Nomascus leucogenys ENSNLEG0000000657816 retrocopies
Oryctolagus cuniculus ENSOCUG000000074472 retrocopies
Otolemur garnettii ENSOGAG0000001040015 retrocopies
Ochotona princeps ENSOPRG000000131154 retrocopies
Pongo abelii ENSPPYG0000000649519 retrocopies
Pan troglodytes ENSPTRG00000007094 16 retrocopies
Pteropus vampyrus ENSPVAG000000040933 retrocopies
Rattus norvegicus ENSRNOG000000076302 retrocopies
Sarcophilus harrisii ENSSHAG000000114941 retrocopy
Sus scrofa ENSSSCG000000249831 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000094086 retrocopies
Tupaia belangeri ENSTBEG000000107509 retrocopies
Tarsius syrichta ENSTSYG000000012711 retrocopy



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