RetrogeneDB ID:

retro_amel_517

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192483.1:1273086..1275054(-)
Located in intron of:ENSAMEG00000006479
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PAPOLA
Ensembl ID:ENSAMEG00000014142
Aliases:None
Description:poly(A) polymerase alpha [Source:HGNC Symbol;Acc:14981]


Retrocopy-Parental alignment summary:






>retro_amel_517
CCGGTGACAACCCCGGGATCACAACAGACGCCGCCGCCGCCCAAGCACTATGGCATCTCCTCCCCCATCAGCCTAGCAGC
CCCCAAGGAGACTGACTGCATACTTACCCAGAAGTTAATTGAAACCCTGAAGCCCTTTGGGGTTTTTGAAGAGGAAGAGG
AACTGCAGCGCAGGATTTTAATTTTGGAAAAATTAAATAATCTGGTAAAGGAATGGATACGAGAAATCAGTGAAAGCAAG
AGCCTTCCACAAACTGTAATTGAAAATGTTGGAGGGAAAATCTTTACATTTGGCTCTTACAGATTAGGAGTACATACGAA
AGGTGCTGATATTGATGCGTTGTGCGTTGCACCGAGACATGTTGATCGAAGTGACTTTTTCACCTCGTTCTATGACAAAT
TGAAACTACACGAAGAAGTAAAAGATTTAAGGGCTGTTGAGGAGGCATTTGTACCAGTTATTAAACTGTGTTTTGATGGT
ATAGAGATTGATATTTTGTTTGCAAGATTGGCACTGCAGACTATTCCAGAAGATTTGGACCTAAGAGATGACAGTCTGCT
TAAAAATTTAGATATTAGATGCATAAGAAGCCTAAACGGTTGCCGGGTGACAGATGAAATTTTACATCTAGTACCAAACA
TTGACAACTTCAGGTTAACTCTGAGAGCCATCAAACTATGGGCGAAATGCCACAATATCTATTCCAATATATTAGGGTTC
CTAGGAGGTGTTTCCTGGGCGATGCTAGTAGCAAGAACTTGCCAGCTCTACCCAAATGCAATAGCATCAACTCTTGTACG
TAAGTTTTTCTTGGTATTTTCTGAATGGGAATGGCCAAATCCAGTGCTACTGAAAGAGCCTGAAGAGCGGAATCTTAATT
TGCCCGTATGGGACCCAAGAGTAAATCCCAGTGATAGGTACCATCTTATGCCCATAATCACACCAGCGTACCCACAGCAG
AACTCCACATACAATGTGTCTGTTTCAACAAGGATGGTCATGATTGAGGAGTTTAAACAAGGGCTTGCTATCACACATGA
AATTTTGCTGAGTAAGGCAGAGTGGTCCAAACTTTTTGAAGCTCCAAGCTTCTTTCAAAAGTACAAGCATTATATTGTAC
TTCTAGCAAGTGCACCAACAGAAAAACAACATCTAGAATGGGTGGGCTTGGTGGAATCAAAAATCCGAATCCTGGTTGGA
AGCTTGGAGAAGAATGAATTTATTACTCTGGCGCATGTGAATCCTCAGTCATTTCCAGCACCTAAAGAAAATCCTGACAA
GGAAGAATTCCGTACGATGTGGGTGATTGGGTTAGTATTAAAAAAGCCAGAAAACTCTGACGTTCTCAGTATTGATCTCA
CCTATGATATCCAGTCTTTCACAGATACGGTTTACAGGCAAGCAATAAATAGCAAGATGTTTGAGATGGATATGAAAATT
GCTGCAATGCATTTAAGGAGAAAGGAACTTCATCAACTATTGCCTAATCATGTGCTTCAGAAGTGGAAAACACATTCAAT
GGAAGGTGTCACTTTAACAGCTTTGAGTGACAGCAGCCTTGACTTGCCTGTGGACACTGAAGACAGCATGTCTGTGCCTT
CACCTGCTAGCACTGTGAAGACCGGCCCAGTGACTGGCAGCTCTCAGGGCAGAAATAGTCCTGCTCCCGCAGCAATGGCA
GCATCAGTGACTGCCGTACAAGTGACTGAGGTTTCCTTGCAACGAGTGAATCCCAGTGAAAGCTTAGGGGGTGCATTGAG
TGAAAGCCTTCCTCAGACTGCCGCACAGCCAGCCCTTCTTCCACCATCAAAGGCCACAGTTGCCAGAGTTGTTTCTTCAA
CATGTCTGGTAAACCATCCACCCAGGCCTTCAGGGAGCACTGCAACAAACGTAGCGAATCCTATAGTGGGAGTCTAGCAG
ACGTTCTCACCTCATGAAGGACCAAGGAAACTCAAAGAAGAGGAACAA

ORF - retro_amel_517 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.42 %
Parental protein coverage: 89.07 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVK
PVTT.GSQQT.PP.KHYGI.SPISLAAPKETDC.LTQKLIETLKPFGVFEEEEELQRRILIL.KLNNLVK
RetrocopyPVTTPGSQQTPPPPKHYGISSPISLAAPKETDCILTQKLIETLKPFGVFEEEEELQRRILILEKLNNLVK
ParentalEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEV
EWIREISESK.LPQ.VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKL.EEV
RetrocopyEWIREISESKSLPQTVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLHEEV
ParentalKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
RetrocopyKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
ParentalVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPN
VPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLV.KFFLVFS.WEWPN
RetrocopyVPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVRKFFLVFSEWEWPN
ParentalPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILL
PVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.EILL
RetrocopyPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHEILL
ParentalSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
SKAEWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
RetrocopySKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
ParentalPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL
PKENPDKEEFRTMWVIGLV.KK.ENS..LS.DLTYDIQSFTDTVYRQAINSKMFE.DMKIAAMH..RK.L
RetrocopyPKENPDKEEFRTMWVIGLVLKKPENSDVLSIDLTYDIQSFTDTVYRQAINSKMFEMDMKIAAMHLRRKEL
ParentalHQLLPNHVLQKKKKHSTEGVRLTPLNDSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGRNSPAPAV
HQLLPNHVLQK.K.HS.EGV.LT.L.DSSLDL..D...SMSVPSP.S..KT.P....GSSQGRNSPAPA.
RetrocopyHQLLPNHVLQKWKTHSMEGVTLTALSDSSLDLPVDTEDSMSVPSPASTVKTGPV--TGSSQGRNSPAPAA
ParentalTAASVTNIQATEVSVLQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPPPRPSGNAA
.AASVT..Q.TEVS...VN.SES.GG..SES.PQTA.QPA..PP.K.TV.RVVSST.LVN.PPRPSG..A
RetrocopyMAASVTAVQVTEVSLQRVNPSESLGGALSESLPQTAAQPALLPPSKATVARVVSSTCLVNHPPRPSGSTA
ParentalTKIPTPIVGVKRTSSPHKEESPKKTKTEEK
T....PIVGV..T.SPH..E.P.K.K.EE.
RetrocopyTNVANPIVGV*QTFSPH--EGPRKLKEEEQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_517 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_517 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000014142 1 retrocopy
retro_amel_517 ,
Bos taurus ENSBTAG000000040541 retrocopy
retro_btau_1078,
Canis familiaris ENSCAFG000000177831 retrocopy
retro_cfam_1783,
Callithrix jacchus ENSCJAG000000065122 retrocopies
retro_cjac_1763, retro_cjac_543,
Homo sapiens ENSG000000900601 retrocopy
retro_hsap_30,
Gorilla gorilla ENSGGOG000000062871 retrocopy
retro_ggor_202,
Myotis lucifugus ENSMLUG000000109221 retrocopy
retro_mluc_1396,
Macaca mulatta ENSMMUG000000186101 retrocopy
retro_mmul_1675,
Monodelphis domestica ENSMODG000000128872 retrocopies
retro_mdom_1714, retro_mdom_1916,
Mustela putorius furoENSMPUG000000030541 retrocopy
retro_mputfur_1375,
Mus musculus ENSMUSG000000211111 retrocopy
retro_mmus_37,
Nomascus leucogenys ENSNLEG000000006251 retrocopy
retro_nleu_2771,
Otolemur garnettii ENSOGAG000000046111 retrocopy
retro_ogar_987,
Pongo abelii ENSPPYG000000061281 retrocopy
retro_pabe_3113,
Pan troglodytes ENSPTRG000000067041 retrocopy
retro_ptro_2595,
Pteropus vampyrus ENSPVAG000000139251 retrocopy
retro_pvam_360,
Vicugna pacos ENSVPAG000000064641 retrocopy
retro_vpac_378,




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