RetrogeneDB ID:

retro_ptro_2339

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:31648977..31650150(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL3L
Ensembl ID:ENSPTRG00000007617
Aliases:None
Description:ribosomal protein L3-like [Source:HGNC Symbol;Acc:10351]


Retrocopy-Parental alignment summary:






>retro_ptro_2339
ATGTCTCACAGAAAGTTCTCCACTCCCAGACATGGGTCCCTCGGCTTCCTGCCTTGGAAGCGCAGCAGCAGGCATCGTGG
GAAGGTGAAGAACTTCCCTAAGGATGACCCGTCCAAGCCGGTCCACCTCACAGCCTTCCTGGGATACAAGGCTGGCATGA
CCCACATCGTGAGGGAAGTCAACAGGCCAGGATCCAAGGTGAACAAGAAGGAGGTGGTGGAGGCTGTGACCATTGTGGAG
AGGCCACCAGTGGGCATTGTGGGCTACGTGGAAACCCCTCAAGGCCTCCGGACTTGCAAGACTGTCTTCGCTGAGCACAT
CAGTGATGAATGCAAGAGGCGTTTCTACAAGAACTGGCAAAAATCTAAGAAGAAGGCCTTTACCAAGTACTGCAAGAAAT
GGCAGGATGAGGATGGCAAGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAAGTCATCCGCGTCATT
GCCCACACCCAGATGCACCTGCTTCCTCTGTGCCAGAAGAAGGCCCACCTGATGGAGATCCAAGTGAATGGAGGCACTGT
GGCTGAGAAGCTGGACTGGGCTGGCGAGAGGCTCAAGCAGCAGGTACCTGTGAACCAAGTGTTTGGGCAGGATGAGATGA
TCGACGTCATCAGGGTGACCAAGGGCAAAGGCTACAAAAGGGTCACCAGTCATTGGCACACCAAGAAGCTGCCCCGCAAG
ACCCACCAAGGCCTGTGCAAGGTGGCCTGTATTGGGGCATGGCATCCTGCTTGTGTGGGCTTCTCTGTGGTACGTGGTGG
GCAGAAAGGCTACCGTCACCGCACTGAGATCAACAAGAAGATCTATAGGATTGGCTAGGGCTACCTTATCAAGGATGGCA
AGCTGATCAAGAACAATGCCTCCACTGACTATGACCTGTCTGACAAGAGCATCAACCCTTTTGGTGGCTTTGTCCACTAT
GGTGAAGTGTCCAATGACTTTGTCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGTGGGTGCTCACCCTCCGCAAGTC
CTTGCTGGTGCAGACAAAGCAGCGGGCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGTTTGGCCATG
GCCGCTTCCGGACCATGGAGGAGAAGAAAGCATTCATGGGACCACTCAAGAAA

ORF - retro_ptro_2339 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.11 %
Parental protein coverage: 96.81 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSHRKFSAPRHGHLGFLPHKRSHRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKR
MSHRKFS.PRHG.LGFLP.KRS.RHRGKVK..P.DDPS.PVHLTAFLGYKAGMTH..REV.RPG.K..K.
RetrocopyMSHRKFSTPRHGSLGFLPWKRSSRHRGKVKNFPKDDPSKPVHLTAFLGYKAGMTHIVREVNRPGSKVNKK
ParentalEEVEAVTIVETPPLMVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDT
E.VEAVTIVE.PP...VG.VGYV.TP.GLR..KT.FAEH.SDEC.RRFYK.W.KSKKKAFTK.CK.W.D.
RetrocopyEVVEAVTIVERPP---VGIVGYVETPQGLRTCKTVFAEHISDECKRRFYKNWQKSKKKAFTKYCKKWQDE
ParentalDGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSV
DGKKQL.KDF..MKKYC.VIRVI.HTQM.LLP..QKKAH.MEIQ.NGGTVAEK..WA..RL..QVPV..V
RetrocopyDGKKQLEKDFSSMKKYCQVIRVIAHTQMHLLPLCQKKAHLMEIQVNGGTVAEKLDWAGERLKQQVPVNQV
ParentalFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTEL
F.Q.E.IDVI.VTKG.G.K.VTS.WHTKKLPRKTH.GL.KVACIGAWHPA.VG.S..R.GQKGY.HRTE.
RetrocopyFGQDEMIDVIRVTKGKGYKRVTSHWHTKKLPRKTHQGLCKVACIGAWHPACVGFSVVRGGQKGYRHRTEI
ParentalNKKIFRIGRGPHMEDGKPVKNNASTSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRKS
NKKI.RIG.G....DGK..KNNAST.YD...KSI.P.GGF.HYGEV.NDFVMLKGC..GTKK.V.TLRKS
RetrocopyNKKIYRIG*GYLIKDGKLIKNNASTDYDLSDKSINPFGGFVHYGEVSNDFVMLKGCVVGTKKWVLTLRKS
ParentalLLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
LLV.....A.E.I.LKFIDTTSKFGHGRF.T..EK.AFMGP.KK
RetrocopyLLVQTKQRALEKIDLKFIDTTSKFGHGRFRTMEEKKAFMGPLKK

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 .38 RPM 0 .02 RPM
SRP007412_cerebellum 0 .43 RPM 0 .00 RPM
SRP007412_heart 0 .12 RPM 38 .27 RPM
SRP007412_kidney 0 .89 RPM 0 .00 RPM
SRP007412_liver 0 .75 RPM 0 .03 RPM
SRP007412_testis 0 .11 RPM 0 .84 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2339 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2339 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2339 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3448

Parental genes homology:
Parental genes homology involve 5 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000084891 retrocopy
Nomascus leucogenys ENSNLEG000000088509 retrocopies
Pongo abelii ENSPPYG000000069731 retrocopy
Pan troglodytes ENSPTRG00000007617 12 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000129212 retrocopies



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