RetrogeneDB ID:

retro_pvam_163

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_1696:216276..217480(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPVAG00000011112
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPVAG00000013189
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pvam_163
CCCAAGCCCGGTCCAGAACCCAGACATCTGCTACAACGAGTTAACAACGAGTGGCAAGATTCAGTCAGCAAGAAGACCTT
CCCAACTGTCAGCCCTGCCACGGGAGAGGTCATAGGCCACGTGGCTGAAGGGGACTGGGCCGATGTGGATCGGGCAGTGA
AAGCGGCCTGGGAGGCCTTCCGCGGAGGGTCTCCATGGCACGGGATGGATACCTCCGAGCGGTCTGGCTGTTGAACCGCT
AGACTGACCTAGTAGAGCTGGATCGTTTCTACTTGGCCTCACTGGAGACCTTGGATAATGAGAAGCCTTTCCAGGAGTCT
TATGTCTTGGACCTGGATGAGGTCATCAAGGTGAACTGGTATTTTGCAGGCTGGGCTGACGAGTGGCATGGCAAGGCCAT
CCCCATGGATGACGAGCATTTCTGCTTTACTCGGCATGAGCCTGTTGGTGTCTGTGGCCAGATAATCCCATGGAATTTCC
CCTTGGTCATGCAGGGCTGGAATCTCGCCCCAGGGCTTGCCACCGGCAATACAGGGGTCTTGAAGATCGCACAGCAGACC
CCCCTCTCTGCCCTGTACGTGGCCTCCCTCATAAAGAGGCGGGATTCCCCACTGGGGTGGTGAACATCCTCACAGGCTAT
GGCAACAACAGGAGCAGCCATCGCCTACCACATGGATATTGACAAAGTTGCCTTCACTGGCTCCACCGAGGTGGGCCACC
TGATCCAGAAGGCAGCCGGAGAGTCCAACCTCAAGAGAGTCACCCTGGAGCTGGGTGGGAAGAGCCCCAGCATTGTGTCG
GCTGATGCTGACATGAGTCACGCTGTGGAGCAGTGCCACAAAGCCCTCTTCAATATGGGCCAGTGCTGCTGTGGCGGTCC
CGGACCTTCACTGAGGAATCCATCTATGATGAGTTTCTCGAGAGAACCGTAGAGAAAGCTGAGCAGAGGAAAGTTGGGAA
TCCCTTTGAGCTGGACACCCAGCAGGGACCCCAGGTGGACAAGGAGCAGTTTGAACGAATCCTCGGATACATCTAGCTTG
ACCAGAAGGAGGGGGCAAAACTTCTCTGCGGTGGAGAGTGTTTTGGGGAGCATGGTTTCTTTATCAAGCCAACAGTCTTT
GGTGATGTGCAGGATGACATGAGGATCACCAAGGAGGAGATCTTTGGGCCTGTGCAGCCCCTGTTCAAGTTCAAGAAGAT
AGAA

ORF - retro_pvam_163 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.12 %
Parental protein coverage: 78.68 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalPAPNQQPEVFYNQIFINNEWHDAVSKKTFPTVNPSTGEVICQVAEGDKEDVDRAVKAARAAFQLGSPWRR
P.P...P.........NNEW.D.VSKKTFPTV.P.TGEVI..VAEGD..DVDRAVKAA..AF..GSPW..
RetrocopyPKPGPEPRHLLQRV--NNEWQDSVSKKTFPTVSPATGEVIGHVAEGDWADVDRAVKAAWEAFRGGSPWHG
ParentalMDASDRGQ-LLNRLADLIERDRTYLAALETLDNGKPYIISYLMDLNKVIKCLRYYAGWADKHHGKTIPID
MD.S.R...LLNR..DL.E.DR.YLA.LETLDN.KP...SY..DL..VIK...Y.AGWAD..HGK.IP.D
RetrocopyMDTSERSG<LLNR*TDLVELDRFYLASLETLDNEKPFQESYVLDLDEVIKVNWYFAGWADEWHGKAIPMD
ParentalGDFFSYTRLEPLGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLI-KEAGFPPG
...F..TR.EP.GVCGQIIPWNFPL.MQ.W.L.P.LATGN..V.K.A.QTPL.ALYVA.LI.KEAGFP.G
RetrocopyDEHFCFTRHEPVGVCGQIIPWNFPLVMQGWNLAPGLATGNTGVLKIAQQTPLSALYVASLI<KEAGFPTG
ParentalVVNIIPGFG-PTAGAAIASHKDVDKVAFTGSTEVGQLIQVAAGSSNLKRVTLELGGKSPNIIMSDADMDW
VVNI..G.G..T..A.IA.H.D.DKVAFTGSTEVG.LIQ.AAG.SNLKRVTLELGGKSP.I...DADM..
RetrocopyVVNILTGYG>TTGAA-IAYHMDIDKVAFTGSTEVGHLIQKAAGESNLKRVTLELGGKSPSIVSADADMSH
ParentalAVEQAHFALFFNQGQCCTAG-SRTFVQEDVYAEFVERSVTRAKSRVVGNPFDSRTEQGPQVDETQFKKIL
AVEQ.H.AL.FN.GQCC..G.SRTF..E..Y.EF.ER.V..A..R.VGNPF...T.QGPQVD..QF..IL
RetrocopyAVEQCHKAL-FNMGQCCCGG<SRTFTEESIYDEFLERTVEKAEQRKVGNPFELDTQQGPQVDKEQFERIL
ParentalGYIKSGKEEGAKLLCGGGAAADRGYFIQPTVFGDVQDSMTIAKEEIFGPVMQILKFKTIE
GYI.....EGAKLLCGG......G.FI.PTVFGDVQD.M.I.KEEIFGPV....KFK.IE
RetrocopyGYI*LDQKEGAKLLCGGECFGEHGFFIKPTVFGDVQDDMRITKEEIFGPVQPLFKFKKIE

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






RNA-Seq - click to see more details

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pteropus vampyrus was not studied using ChIP-Seq data.

EST - click to see more details

Pteropus vampyrus was not studied using EST data.

TSS - click to see more details

Pteropus vampyrus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pvam_163 was not experimentally validated.

Retrocopy orthology:
Pteropus vampyrus 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 21 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136641 retrocopy
retro_amel_51,
Bos taurus ENSBTAG000000087431 retrocopy
retro_btau_48,
Canis familiaris ENSCAFG000000086831 retrocopy
retro_cfam_1493,
Equus caballus ENSECAG000000176732 retrocopies
retro_ecab_1054, retro_ecab_1061,
Felis catus ENSFCAG000000220001 retrocopy
retro_fcat_1590,
Homo sapiens ENSG000001112751 retrocopy
retro_hsap_19,
Gorilla gorilla ENSGGOG000000071081 retrocopy
retro_ggor_33,
Latimeria chalumnae ENSLACG000000117981 retrocopy
retro_lcha_108,
Microcebus murinus ENSMICG000000034871 retrocopy
retro_mmur_19,
Myotis lucifugus ENSMLUG000000170841 retrocopy
retro_mluc_1918,
Macaca mulatta ENSMMUG000000083361 retrocopy
retro_mmul_247,
Mustela putorius furoENSMPUG000000022821 retrocopy
retro_mputfur_27,
Mus musculus ENSMUSG000000294551 retrocopy
retro_mmus_222,
Nomascus leucogenys ENSNLEG000000000161 retrocopy
retro_nleu_22,
Otolemur garnettii ENSOGAG000000330931 retrocopy
retro_ogar_203,
Pongo abelii ENSPPYG000000049661 retrocopy
retro_pabe_32,
Pteropus vampyrus ENSPVAG00000013189 1 retrocopy
retro_pvam_163 ,
Rattus norvegicus ENSRNOG000000013441 retrocopy
retro_rnor_307,
Sus scrofa ENSSSCG000000098891 retrocopy
retro_sscr_9,
Ictidomys tridecemlineatus ENSSTOG000000150091 retrocopy
retro_itri_33,
Xenopus tropicalis ENSXETG000000209301 retrocopy
retro_xtro_12,


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