RetrogeneDB ID:

retro_pabe_1652

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:19:59109110..59109891(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7A
Ensembl ID:ENSPPYG00000019730
Aliases:None
Description:ribosomal protein L7a [Source:HGNC Symbol;Acc:10364]


Retrocopy-Parental alignment summary:






>retro_pabe_1652
GCCAAGGAGAAGAAGGTGACCCCAGTCCCTGCTGTCATGAAGAAGCAGGAGACCATGAAACTGGTGAATCCTCTGTTTGA
GAAAAGGCCTAAGAATCTTGGCACTGGATAGGACATCCAACCCAAACGGACCTCACCCGCTTTGTCAAATGGTCCCACTA
TATCACGTTGCAGTGGCAAAGAACCATTCTCTCTGTGAGTGGCTGAAAGTGCCTCCTGCAATCAGCCAGTTCATCCAGGC
CTCAGACTGTCACGCAGCCACCCAACTGCTTAAGCTGGCCCAGTACAGACCAGAGGCAAAGCAGAAGGAGAAGCAGAGAC
TGTTATCCTGGGCTAAGAAGAAAGCTGTCAGCAAAGGGGACACCCCCACGAAGAGACCACTCATCCTTCAAACAGGGTTA
ACACTGCCACCACCGTGTTCATGCACAGCAAGAAGGTTCATCTGATGGTGACTGCATGTGACATGGATCCCAGCAAGCTG
TCTGTCTTCCTACCTGCCCTGGGTCATAAGATGGGAGTTCCTGACTACATTAATGAGGGGAAGGCAAGACTGGGATACTG
AGTCCACAGGAAGACCAGCACCACTGTTACCTTCACACCAGTTAACTTGGGAGACAAAGGAGCTTTGGCTAAGCTGGTGG
AAGCTACCAGGACCAATTAAATTAACAGATATGATGAGATCTGTAGTCACTGGGGAGGCAACATCCTGGGTCCAAAATCC
CTGGGATGCATTGCCAAAGCTGGAAAAGGCAAAGGCTAAAGAACTTGCCACCAAACTGGGT

ORF - retro_pabe_1652 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.15 %
Parental protein coverage: 97.74 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAI-LYKRLK
AK.KKV.P.PAV.KKQE..K.VNPLFEKRPKN.G.G.DIQPKR........P...R........L...LK
RetrocopyAKEKKVTPVPAVMKKQETMKLVNPLFEKRPKNLGTG*DIQPKRTSPALSNGPTISRCSGKEPF>LCEWLK
ParentalVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAG-VNTVT
VPPAI.QF.QA.D...ATQLLKLA..YRPE.KQ..KQRLL..A.KKA..KGD.PTKRP..L..G.VNT.T
RetrocopyVPPAISQFIQASDCHAATQLLKLA-QYRPEAKQKEKQRLLSWAKKKAVSKGDTPTKRPLILQTG<VNTAT
ParentalTL-VENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKG
T.....KK..L.V.A.D.DP..L.VFLPAL..KMGVP..I..GKARLG..VHRKT.TTV.FT.VN..DKG
RetrocopyTVFMHSKKVHLMVTACDMDPSKLSVFLPALGHKMGVPDYINEGKARLGY*VHRKTSTTVTFTPVNLGDKG
ParentalALAKLVEAIRTNYNDRYDEIRRHWGGNILGPKSVARIA-KLEKAKAKELATKLG
ALAKLVEA.RTN...RYDEI..HWGGNILGPKS...IA.KLEKAKAKELATKLG
RetrocopyALAKLVEATRTN*INRYDEICSHWGGNILGPKSLGCIA>KLEKAKAKELATKLG

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 169 .30 RPM
SRP007412_cerebellum 0 .00 RPM 97 .28 RPM
SRP007412_heart 0 .00 RPM 150 .31 RPM
SRP007412_kidney 0 .00 RPM 335 .58 RPM
SRP007412_liver 0 .00 RPM 292 .34 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1652 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1652 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1652 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 27 parental genes, and 378 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001170829 retrocopies
Canis familiaris ENSCAFG0000001768036 retrocopies
Callithrix jacchus ENSCJAG000000148273 retrocopies
Cavia porcellus ENSCPOG000000013244 retrocopies
Dasypus novemcinctus ENSDNOG000000244248 retrocopies
Dipodomys ordii ENSDORG000000064713 retrocopies
Equus caballus ENSECAG000000085482 retrocopies
Erinaceus europaeus ENSEEUG000000002032 retrocopies
Felis catus ENSFCAG0000000582520 retrocopies
Gorilla gorilla ENSGGOG0000001444248 retrocopies
Loxodonta africana ENSLAFG000000064362 retrocopies
Macropus eugenii ENSMEUG0000001455016 retrocopies
Myotis lucifugus ENSMLUG0000000466610 retrocopies
Macaca mulatta ENSMMUG000000223419 retrocopies
Monodelphis domestica ENSMODG000000127543 retrocopies
Mustela putorius furoENSMPUG0000001239813 retrocopies
Mus musculus ENSMUSG0000006264710 retrocopies
Nomascus leucogenys ENSNLEG0000001306822 retrocopies
Otolemur garnettii ENSOGAG0000001402716 retrocopies
Ochotona princeps ENSOPRG000000057264 retrocopies
Pongo abelii ENSPPYG00000019730 52 retrocopies
Rattus norvegicus ENSRNOG0000004909710 retrocopies
Sarcophilus harrisii ENSSHAG000000043374 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000036713 retrocopies
Tupaia belangeri ENSTBEG0000000859526 retrocopies
Tarsius syrichta ENSTSYG0000000546720 retrocopies
Tursiops truncatus ENSTTRG000000076453 retrocopies



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