RetrogeneDB ID:

retro_ptro_776

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:12:87938208..87939488(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MKRN1
Ensembl ID:ENSPTRG00000019766
Aliases:None
Description:makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]


Retrocopy-Parental alignment summary:






>retro_ptro_776
ATGGCGGAGGCTGCAGCTCTCAGACCAACAGCCACAACATCAGGGGCGGGAGTGGCGGCAGCGGTGGCGGCAGCAGCGGC
CTCCCCTACCAGGATCCCCACCGTCACCATTCTGTCCCCAGGGGGCAGGCGAGGGGGCCGCGGCAGCGATGGCAGCGGCG
GCAGCTGGACTAAACATGTCACCTGCAGGTATTTTATGCATGGGGTTTATAAGGAAGGAGATAACTGTTGCAAGTTGCAT
GACCTCTCTGACAGTCCGTATAATGTAGTGTACAAGAGTTTGCAGCGAGGGTACTGTATTTATGGAGACTGCTGCAGATA
TGAACATAGCAAGCCATTGAAACAGAAAGAAGCAACTGCTGTAGAGCTAACTACAAAGTCGTCCCTTGCTGCTTCCTCAA
GTCTCTCATGGATAGTCGGACCACTTGTTGAAATGAATACGGGTGAAGCTGAGTCAAGAAATTCAAACTTTGTAACTGTA
GGAGCAGGTTCAGAGGGCTGGGTGAATGCTGTTGAGTTTGTTCCTGGGCAACCCTACTGTGGCCGCACTGCGCCTTCCTG
CACTGAAGCACCCCTGCAGGGCTCAGTGACCAAGGAAGAATCAGAGAAAGAGCAAACTGCCGTGGAAACAAAGAAGCAGC
TGTGCCCCTATGCTGCAGTGGGAGAGTGCCGATATCGGGAGAACTTGTGTGTATACGGAGATTCGTGTGACATGTGTGGC
TGCAGGTCCTGCATCTGATGGATGCTGCCCAGAGATCACAGCATATAAAATCGTGCTTTGAGGCCCATGAGAAAGACATG
GAGCTCTCATTTGCTGTGCAGCGCAGTGAGGAAATGGTGTGTGAGAGCTGCATGGAGATGATCTATGAGAAAGCCAACCC
CAGAGAGCACCGCTTCGGGATCCTCTTCAACTGCAACCACACCTACTGTCTTAAGTGCATTCGCAAGTGGAGGAGTGCTA
AGCAGTTTGAGAGCAAGATCATAAAGTCCTGCCCAGAATGTCGGATCACATCTAACTTTGTCATTCCAAGTGAGTACTGT
GTGGAGGAGAAAGAAGAGAAGCAGAAACTCATTCTGAAATACAAGGAGGCAATGAGCAACAAGGCATGCAGGTATTTTGA
TGAAGGACATGGGAGCTGTCCGTTTGGAGGGAACAGTTTTTATAAGCATGTGTACCCTGATGGCCGTAGAGAGGAGCCAC
AGAGACAGAAAGTGGGAACATCAAGCAGATACCCGGCCCAATGAAGGAACCACTTCTGGGAACTCATTGAGGAAAGAGAA

ORF - retro_ptro_776 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.67 %
Parental protein coverage: 88.59 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAEAAAPGTTATTSGAGAAAATAAAA-SPTPIPTVTAPSLGAGGGGGGSDGSGGGWTKQVTCRYFMHGVC
MAEAAA...TATTSGAG.AAA.AAAA.SPT.IPTVT..S.G...GG.GSDGSGG.WTK.VTCRYFMHGV.
RetrocopyMAEAAALRPTATTSGAGVAAAVAAAAASPTRIPTVTILSPGGRRGGRGSDGSGGSWTKHVTCRYFMHGVY
ParentalKEGDNCRYSHDLSDSPYSVVCKYFQRGYCIYGDRCRYEHSKPLKQEEATATELTTKSSLAASSSLSSIVG
KEGDNC...HDLSDSPY.VV.K..QRGYCIYGD.CRYEHSKPLKQ.EATA.ELTTKSSLAASSSLS.IVG
RetrocopyKEGDNCCKLHDLSDSPYNVVYKSLQRGYCIYGDCCRYEHSKPLKQKEATAVELTTKSSLAASSSLSWIVG
ParentalPLVEMNTGEAESRNSNFATVGAGSEDWVNAIEFVPGQPYCGRTAPSCTEAPLQGSVTKEESEKEQTAVET
PLVEMNTGEAESRNSNF.TVGAGSE.WVNA.EFVPGQPYCGRTAPSCTEAPLQGSVTKEESEKEQTAVET
RetrocopyPLVEMNTGEAESRNSNFVTVGAGSEGWVNAVEFVPGQPYCGRTAPSCTEAPLQGSVTKEESEKEQTAVET
ParentalKKQLCPYAAVGECRYGEN-CVYIHGDSCDMCG-LQVLHPMDAAQRSQHIKSCIEAHEKDMELSFAVQRSK
KKQLCPYAAVGECRY.EN.CVY..GDSCDMCG.LQVLH.MDAAQRSQHIKSC.EAHEKDMELSFAVQRS.
RetrocopyKKQLCPYAAVGECRYRENLCVY--GDSCDMCG<LQVLHLMDAAQRSQHIKSCFEAHEKDMELSFAVQRSE
ParentalDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPSEYW
.MVC..CME..YEKANP.E.RFGIL.NCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPSEY.
RetrocopyEMVCESCMEMIYEKANPREHRFGILFNCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPSEYC
ParentalVEEKEEKQKLILKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAYPDGRREEPQRQKVGTSSRYRAQRRN
VEEKEEKQKLILKYKEAMSNKACRYFDEG.GSCPFGGN.FYKH.YPDGRREEPQRQKVGTSSRY.AQ.RN
RetrocopyVEEKEEKQKLILKYKEAMSNKACRYFDEGHGSCPFGGNSFYKHVYPDGRREEPQRQKVGTSSRYPAQ*RN
ParentalHFWELIEERE
HFWELIEERE
RetrocopyHFWELIEERE

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 .02 RPM 62 .44 RPM
SRP007412_cerebellum 0 .07 RPM 123 .61 RPM
SRP007412_heart 0 .00 RPM 87 .53 RPM
SRP007412_kidney 0 .03 RPM 90 .01 RPM
SRP007412_liver 0 .00 RPM 52 .73 RPM
SRP007412_testis 4 .74 RPM 1105 .68 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_776 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_776 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_776 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1140
Pongo abelii retro_pabe_947

Parental genes homology:
Parental genes homology involve 19 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000083062 retrocopies
Canis familiaris ENSCAFG000000039532 retrocopies
Choloepus hoffmanni ENSCHOG000000110153 retrocopies
Callithrix jacchus ENSCJAG000000134742 retrocopies
Cavia porcellus ENSCPOG000000009481 retrocopy
Dasypus novemcinctus ENSDNOG000000195642 retrocopies
Felis catus ENSFCAG000000249421 retrocopy
Homo sapiens ENSG000001336064 retrocopies
Gorilla gorilla ENSGGOG000000239774 retrocopies
Microcebus murinus ENSMICG000000021141 retrocopy
Macaca mulatta ENSMMUG000000104203 retrocopies
Mus musculus ENSMUSG000000299221 retrocopy
Nomascus leucogenys ENSNLEG000000019214 retrocopies
Otolemur garnettii ENSOGAG000000098772 retrocopies
Pongo abelii ENSPPYG000000180573 retrocopies
Pan troglodytes ENSPTRG00000019766 5 retrocopies
Sus scrofa ENSSSCG000000164982 retrocopies
Tarsius syrichta ENSTSYG000000099963 retrocopies
Tursiops truncatus ENSTTRG000000095282 retrocopies



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