RetrogeneDB ID:

retro_pabe_1861

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:21:37201090..37202298(-)
Located in intron of:ENSPPYG00000011401
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL3
Ensembl ID:ENSPPYG00000011837
Aliases:None
Description:ribosomal protein L3 [Source:HGNC Symbol;Acc:10332]


Retrocopy-Parental alignment summary:






>retro_pabe_1861
ATGTCTCACAGACAGTTCTCCACTCCCAGACATGGGTCCCTCTGCTTCCTGACATGGGAGCACAGAAATAGGCATCGTCG
GAAGGTGAAGAGCTTCCCCAAGGATGCCCCTTCCAAGCCGGTCAACGTCACAGCCTTGCTGGGATACAAGGCTGGCACGA
CCCACATCACATGGGAAGTCAACAGGCCAGGACCCAAGGTGAAAGAGAAGGAGGTGGCAGAGGCCGTGACTACTGTGGAG
ACACCACCTATGGTGGTTATGGGCATTGTGGGCTACGTGGAAACCCCTTGAGGCCTCTGGACCTTCAAGACTATCTTTGC
TGGGCACATCAATGATGAGTGCAAAAGGCGTTTCTCTAACAACTGGCATAAATCTAGGAAGAAGGCCTTTACCAAGTACT
GCAAGAAATGGCAGGATGACGATGGCAAGAAGCAGCCAGAGAAGACTTCAGCAGCATGAGGAAGCACTGCCAAGTCACCC
GCGTTGCTGCCCACACCCAGACGCGCCTGCTTCCTCTGCGCCAGAAGAAGGCTCAACTGATGGAGATCCAAGTGAATGGA
GGCACCACGGCTGAGAAGCTGGACTGGGCCCAGGAGGGGCTAGAGCAGCAGGTATCTGTGAACCAAGCATTTGGGCTGGA
TGAGATGATCGACATCACCGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGTTGTTGGCACAACAAGAAGCTGC
CCCACAAGACCCACCGAGGCCTGTGCAAGGTGGCCTGGATTGGGGCATGGCATCCTGCCCACGTGGCCTTCTCCATGGCA
TGAGCTGGGCAGAAAGGCGACCACCACCGCACTGAGATCAACAAGAAGATCTGTAAGATCGGCCAGGGCTACCTTACTGA
GGACAGCAAACTGATCAAGAACAATGCCTCCACTGACTATGTCCTGTCTGACAAGAGCATCAACCCTCTGGGTGGCTTTG
TCCACTATGGTGAAGTGACCAATAACTCTGTCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGCGAGTGCTCATTCTG
TGCACATCTTTGCTGGTGCAGACCAGATGGTGGGCTCTGGAGAAGACTGACCTTAAGTTCACTGATACCACCTCCAAGTT
TGGCCATGGCCACTTCCAGACCATGGAGGAGAAGAAAGCATTCATGGGACCACTCAAGGAAGACCGAATTGCAAAGGAAG
AAGGAGCT

ORF - retro_pabe_1861 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.44 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
MSHR.FS.PRHGSL.FL......RHR.KVKSFPKD.PSKPV..TA.LGYKAG.THI..EV.RPG.KV..K
RetrocopyMSHRQFSTPRHGSLCFLTWEHRNRHRRKVKSFPKDAPSKPVNVTALLGYKAGTTHITWEVNRPGPKVKEK
ParentalEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDE
EV.EAVT.VETPPMVV.GIVGYVETP.GL.TFKT.FA.HI.DECKRRF..NWHKS.KKAFTKYCKKWQD.
RetrocopyEVAEAVTTVETPPMVVMGIVGYVETP*GLWTFKTIFAGHINDECKRRFSNNWHKSRKKAFTKYCKKWQDD
ParentalDGKKQLEK-DFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQ
DGKKQ.EK.DFSSM.K.CQV.RV.AHTQ.RLLPLRQKKA.LMEIQVNGGT.AEKLDWA.E.LEQQV.VNQ
RetrocopyDGKKQPEK<DFSSMRKHCQVTRVAAHTQTRLLPLRQKKAQLMEIQVNGGTTAEKLDWAQEGLEQQVSVNQ
ParentalVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTE
.FG.DEMID..GVTKGKGYKGVTS.WH.KKLP.KTHRGL.KVA.IGAWHPA.VAFS.A.AGQKG.HHRTE
RetrocopyAFGLDEMIDITGVTKGKGYKGVTSCWHNKKLPHKTHRGLCKVAWIGAWHPAHVAFSMA*AGQKGDHHRTE
ParentalINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRK
INKKI.KIGQGYL..D.KLIKNNASTDY.LSDKSINPLGGFVHYGEVTN..VMLKGCVVGTKKRVL.L..
RetrocopyINKKICKIGQGYLTEDSKLIKNNASTDYVLSDKSINPLGGFVHYGEVTNNSVMLKGCVVGTKKRVLILCT
ParentalSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
SLLVQT...ALEK.DLKF.DTTSKFGHG.FQTMEEKKAFMGPLK.DRIAKEEGA
RetrocopySLLVQTRWWALEKTDLKFTDTTSKFGHGHFQTMEEKKAFMGPLKEDRIAKEEGA

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 .06 RPM 169 .41 RPM
SRP007412_cerebellum 0 .24 RPM 139 .11 RPM
SRP007412_heart 0 .00 RPM 60 .51 RPM
SRP007412_kidney 0 .00 RPM 379 .03 RPM
SRP007412_liver 0 .00 RPM 256 .93 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1861 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1861 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1861 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2529
Pan troglodytes retro_ptro_1473
Gorilla gorilla retro_ggor_1582

Parental genes homology:
Parental genes homology involve 29 parental genes, and 143 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000108531 retrocopy
Bos taurus ENSBTAG000000032283 retrocopies
Canis familiaris ENSCAFG000000013461 retrocopy
Callithrix jacchus ENSCJAG000000162766 retrocopies
Dasypus novemcinctus ENSDNOG000000011214 retrocopies
Equus caballus ENSECAG000000206651 retrocopy
Erinaceus europaeus ENSEEUG000000146612 retrocopies
Echinops telfairi ENSETEG000000113805 retrocopies
Felis catus ENSFCAG000000058201 retrocopy
Homo sapiens ENSG000001003169 retrocopies
Gorilla gorilla ENSGGOG0000000232610 retrocopies
Macropus eugenii ENSMEUG0000000978926 retrocopies
Microcebus murinus ENSMICG000000158321 retrocopy
Myotis lucifugus ENSMLUG000000237111 retrocopy
Monodelphis domestica ENSMODG000000095392 retrocopies
Mustela putorius furoENSMPUG000000132713 retrocopies
Mus musculus ENSMUSG0000006003630 retrocopies
Nomascus leucogenys ENSNLEG000000152342 retrocopies
Oryctolagus cuniculus ENSOCUG000000277124 retrocopies
Otolemur garnettii ENSOGAG000000000327 retrocopies
Ochotona princeps ENSOPRG000000130883 retrocopies
Procavia capensis ENSPCAG000000106421 retrocopy
Pongo abelii ENSPPYG000000069731 retrocopy
Pongo abelii ENSPPYG00000011837 10 retrocopies
Pteropus vampyrus ENSPVAG000000032042 retrocopies
Rattus norvegicus ENSRNOG000000168962 retrocopies
Sarcophilus harrisii ENSSHAG000000032122 retrocopies
Tupaia belangeri ENSTBEG000000059891 retrocopy
Tursiops truncatus ENSTTRG000000108802 retrocopies



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