RetrogeneDB ID:

retro_pvam_1347

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:scaffold_658:289332..290227(-)
Located in intron of:ENSPVAG00000011562
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSPVAG00000008774
Aliases:None
Description:UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12) [Source:HGNC Symbol;Acc:19877]


Retrocopy-Parental alignment summary:






>retro_pvam_1347
CCTGTTATAGACACCATTGATTGGAATACTTTTGAATTCTATATGCAGACTGGAGAACCCATGATTGGCGGGTTTGACTG
GCGTTTAACATTCCAGTGGCATTCTGTCCCCAAACATGAAAGGGACAGGTGGAAATCGAGAATTGACCCAATCAGATCGC
CCACCATGGCAGGAGGACTATTTGCTGTCAGCAAGAAATATTTTGAGTACCTTGGAACATATGACACTGGAATGGAAGTG
TGGGGAGGTGAAAACCTCGAGCTGTCTTTTCGAGTGTGGCAGTGTGGAGGTAAATTGGAGATCCACCCGTGTTCCCACGT
GGGCCATGTATTCCCCAAGCGGGCACCATATGCTCGGCCCAATTTCCTACAGAATACTGCTCGGGCAGCGGAAGTGTGGA
TGGATGAGTACAAAGAGCATTTCTACAATCGGAGCCCTCCAGCAGGAAAGATGCTTATGGTGATATTTCTGAAAGAAAAT
TACTACGAGAACGGCTGACTGCAAAAGCTTTGACTGGTATTTGAAAAATGTGTTTTCGAATTTACATGTTCCAGAGGATA
GGCCAGGCTGGCACGGAGCTATTCGCAGTATGGGGATCTCTTCTGAATGTTTAGATTATAATTCTCCTGACAACAACCCC
ACAGGTGCTAACCTTTCACTGTTTGGATGCCATGGTCAAGGAGGCAATCAGTTCTTTGAATATACTTCAAACAAAGAAAT
ACGGTTTAATTCTGTGACAGAGTTATGTGCGGAGGTTCCTGAGCAAAAGAATCATGTAGGAATGCAGAATTGTCCAAAAG
ATGGGTTCCCTGTTCCAGCAAACATTATTTGGCATTTTAAAGAAGATGGGACCATTTTTCATCCACACTCAGGACTTTGT
GTTAGTGCTTATCGG

ORF - retro_pvam_1347 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.09 %
Parental protein coverage: 51.3 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPVIDVIDWNT-EYLGTLGEPHIGD-DWRLVFTWHVVPTRERMRMRSPIDVIRSPTMAGGLFAVSKKYFEY
PVID.IDWNT.E.....GEP.IG..DWRL.F.WH.VP..ER.R..S.ID.IRSPTMAGGLFAVSKKYFEY
RetrocopyPVIDTIDWNTFEFYMQTGEPMIGGFDWRLTFQWHSVPKHERDRWKSRIDPIRSPTMAGGLFAVSKKYFEY
ParentalLGSYDTGMEVWGGENLEFSFRIWQCGGTLEIHPCSHVGHVFPKQAPYSRTKALANSVRAAEVWMDEFKEL
LG.YDTGMEVWGGENLE.SFR.WQCGG.LEIHPCSHVGHVFPK.APY.R...L.N..RAAEVWMDE.KE.
RetrocopyLGTYDTGMEVWGGENLELSFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDEYKEH
ParentalYYHRNPHA-RLEPFGDVTERRQLRAKL-QCKDFKWFLETVYPELHVPEDRPGFFGMLQNKGLKDYCFDYN
.Y.R.P.A.R....GD..ER..LR..L..CK.F.W.L..V...LHVPEDRPG..G.....G....C.DYN
RetrocopyFYNRSPPA<RKDAYGDISERKLLRERL<DCKSFDWYLKNVFSNLHVPEDRPGWHGAIRSMGISSECLDYN
ParentalPPNEHDITGHQVHLYLCHGMGQNQFFEYTSQREIRYNTHQPEACIAVEAGTDILIMHLCEE---TAPENQ
.P.....TG....L..CHG.G.NQFFEYTS..EIR.N....E.C..V........M..C.......P.N.
RetrocopySP-DNNPTGANLSLFGCHGQGGNQFFEYTSNKEIRFNS-VTELCAEVPEQKNHVGMQNCPKDGFPVPANI
ParentalKFILQEDGSLFHIQSNKCVQAER
.....EDG..FH..S..CV.A.R
RetrocopyIWHFKEDGTIFHPHSGLCVSAYR

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_1347 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 33 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000023021 retrocopy
retro_acar_54,
Ailuropoda melanoleuca ENSAMEG000000045201 retrocopy
retro_amel_93,
Anas platyrhynchos ENSAPLG000000121971 retrocopy
retro_apla_8,
Bos taurus ENSBTAG000000090371 retrocopy
retro_btau_1410,
Canis familiaris ENSCAFG000000024941 retrocopy
retro_cfam_683,
Cavia porcellus ENSCPOG000000124181 retrocopy
retro_cpor_1467,
Equus caballus ENSECAG000000165461 retrocopy
retro_ecab_52,
Ficedula albicollis ENSFALG000000051881 retrocopy
retro_falb_8,
Felis catus ENSFCAG000000088311 retrocopy
retro_fcat_126,
Gorilla gorilla ENSGGOG000000057921 retrocopy
retro_ggor_890,
Loxodonta africana ENSLAFG000000220111 retrocopy
retro_lafr_536,
Meleagris gallopavo ENSMGAG000000072441 retrocopy
retro_mgal_1,
Microcebus murinus ENSMICG000000110751 retrocopy
retro_mmur_282,
Myotis lucifugus ENSMLUG000000026301 retrocopy
retro_mluc_804,
Macaca mulatta ENSMMUG000000195611 retrocopy
retro_mmul_888,
Mustela putorius furoENSMPUG000000065021 retrocopy
retro_mputfur_569,
Mus musculus ENSMUSG000000397741 retrocopy
retro_mmus_183,
Nomascus leucogenys ENSNLEG000000170191 retrocopy
retro_nleu_940,
Oryctolagus cuniculus ENSOCUG000000162211 retrocopy
retro_ocun_1260,
Otolemur garnettii ENSOGAG000000014082 retrocopies
retro_ogar_3253, retro_ogar_717,
Ochotona princeps ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG000000194371 retrocopy
retro_pabe_949,
Pelodiscus sinensis ENSPSIG000000172461 retrocopy
retro_psin_1,
Pan troglodytes ENSPTRG000000211801 retrocopy
retro_ptro_777,
Pteropus vampyrus ENSPVAG00000008774 1 retrocopy
retro_pvam_1347 ,
Rattus norvegicus ENSRNOG000000080993 retrocopies
retro_rnor_1084, retro_rnor_1085, retro_rnor_2453,
Sarcophilus harrisii ENSSHAG000000174741 retrocopy
retro_shar_44,
Sus scrofa ENSSSCG000000053791 retrocopy
retro_sscr_32,
Ictidomys tridecemlineatus ENSSTOG000000213061 retrocopy
retro_itri_41,
Tupaia belangeri ENSTBEG000000036271 retrocopy
retro_tbel_2065,
Tarsius syrichta ENSTSYG000000049751 retrocopy
retro_tsyr_386,
Tursiops truncatus ENSTTRG000000108481 retrocopy
retro_ttru_212,




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