RetrogeneDB ID:

retro_ptro_2501

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:161189994..161191065(-)
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_2501
TCCAAGCCGGTCCACCTCACAGCCTTCCTGGGATACAAGGCTGGCATGACTCACATCGTGCGGGAAGTCGACAGGCCAGG
ATCCAAGGTGAACAAGAAGGAGGTGGTGGAGGCTGTGACCATTGTAGAGACACCACCCATGGTGGTTGTGGGCATTGTGG
GCTACGTGGAAACCCCTCGAGGCCTCCGGACCTTCAAGACTGTCTTTGCTGAGCACATCAGTGATGAATGCAAGAGGCGT
TTCTATAAGAATTGGCATAAATCTAAGAAGAAGGCCTTTACCAAGTACTGCAAGAAATGGCAGGATGAGGATGACAAGAA
GCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAAGTCATCCGTGTCATTGCCCACACCCAGATGCGCCTGC
TTCCTCTGCGCCAGAAGAAGGCCCACCTGATGGAGATCCAGGTGAACGGAGGCACCGTGGCCGAGAAGCTGGACTGGGCC
CGCGAGAGGCTCGAGCAGCAGGTACCTGTGAACCAAGTGTTTGGGCAGGATGAGATGATCGACGTCATCGGGGTGACCAA
GGGCAAAGGCTACAAAGGGGTCACCAGTCGTTGGCACACCAAGAACCTGCCCCGCAAGACCCACCAAGGCCTGCGCAAGG
TGGCCTGTATTGGGGCATGGCATCCTGCTCGTGTAGCCTTCTCTGTGGCACGCGCTGGGCAGAAAGGCTACCATCACCGC
ACTGAGATCAACAAGAAGATCTATAAGATTGGCCAGGGCTACCTTATCAAGGATGGCAAGCTGATCAAGAACAATGCCTC
CACTGACTATGACCTATCTGACAAGAGCATCAACCCTCTGGGTGGCTTTGTCCACTATGGTGAAGTGACCAATGACTTTG
TCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGCGGGTGCTCACCCTCCGCAAGTCCTTGCTGGTGCAGACGAAGCGG
CGGGCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGTTTGGCCATGGCCGCTTCCAGACCATGGAGGA
GAAGAAAGCATTCATGGGACCACTCAAGAAA

ORF - retro_ptro_2501 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.31 %
Parental protein coverage: 87.71 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKREEVEAVTIVETPPLMVVGVVGYVATPRGLRSFKTIFA
S.PVHLTAFLGYKAGMTH..REV.RPG.K..K.E.VEAVTIVETPP..VVG.VGYV.TPRGLR.FKT.FA
RetrocopySKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFA
ParentalEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDTDGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKK
EH.SDEC.RRFYK.WHKSKKKAFTK.CK.W.D.D.KKQL.KDF..MKKYC.VIRVI.HTQM.LLP.RQKK
RetrocopyEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDDKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKK
ParentalAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSVFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKG
AH.MEIQ.NGGTVAEK..WA..RLE.QVPV..VF.Q.E.IDVI.VTKG.G.KGVTSRWHTK.LPRKTH.G
RetrocopyAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKNLPRKTHQG
ParentalLRKVACIGAWHPARVGCSIARAGQKGYHHRTELNKKIFRIGRGPHMEDGKPVKNNASTSYDVTAKSITPL
LRKVACIGAWHPARV..S.ARAGQKGYHHRTE.NKKI..IG.G....DGK..KNNAST.YD...KSI.PL
RetrocopyLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPL
ParentalGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRKSLLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRA
GGF.HYGEV.NDFVMLKGC..GTKKRV.TLRKSLLV...R.A.E.I.LKFIDTTSKFGHGRFQT..EK.A
RetrocopyGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKA
ParentalFMGPQKK
FMGP.KK
RetrocopyFMGPLKK

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 123 .39 RPM 0 .02 RPM
SRP007412_cerebellum 88 .19 RPM 0 .00 RPM
SRP007412_heart 25 .68 RPM 38 .27 RPM
SRP007412_kidney 149 .98 RPM 0 .00 RPM
SRP007412_liver 101 .21 RPM 0 .03 RPM
SRP007412_testis 21 .18 RPM 0 .84 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2501 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2501 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2501 has 0 orthologous retrocopies within eutheria group .


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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