RetrogeneDB ID: retro_pvam_9

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_1973:135179..136490(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000012223
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSPVAG00000006834
• Aliases: None
• Description: PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]

Sequence

>retro_pvam_9
ATGGTCCACCTGCTGTCCTCCGAAGTGCGGCAGCTGCTCCACAACAAATTCGTCGTCGTCCTGGGAGATTCCGTCCAGAG
GTCCGTGTACAAGGACCTGGTGCTCCTGTTGCAGAAAGATTGCCTGCTCACTCACAGACAGCTCAAGGTCAAGGGGGAGA
TGAGCTTTGAACAGGATGAGCTGGTGGTCGGAGGCCAGAAGAGCCCCATGCACAACCGCACCAGCTACCGCGAGGTCCGC
CAGTACTGCTCCGGCCACCATCTGGTGCGTTTCTACTTCCTCACGCGCGTCTACAACGAGTATGTCCAGGGCGTCTTGGA
AGAGCTGCAGGCCGACAAGCACACCCCGGACGTGGTCATCATTAACTCCTGCCTCTGGGACATCTCCAGGTACGGACAGG
ACTCCGTTAGGAGCTACCGGGAGAACCTGGAGAACCTGTTCCGGCACCTAGGCCAGGTGCTGCCGGAGTCATGCCTCCTG
GTGTGGAACACGGCCATGCCGGTTGGCGAGAAAATCACCGGGGGCTTCCTCCTGCCGGAGCAGCAGTCCTTGGCCCTCCG
CCTGAGACTCGGCGTGATTGAAGCCAACTTCTACAGCTCTGCTGAGGCGGGGAAGCACGGTTTCGACGTGTTGGACTTGC
ATTTCCACTTCCGCCATGCGGAGAAGCACCGGCAGGGAGACGGGGTGCATTGGAACCAATACGCGCACCGACAGCTCTCC
CAGCTCCTGCTGGCCCACGTGGCCGACGCCTGGGGTGTGGAGCTCCCCAACCGCGACCCAGTGGGCAAGTGGATCAAGGC
AGGCCGTGCGACAGGAGAACCTGGCCTGGGAGTCGAGAGGCAGGCCCAGGCCAGCAGAGATCCACAGGTCTTGCTCCCGA
CCCCATCGTTGCCTCCCCGTAGGCTGCGCCCCCTGCTCCCGCTCCCAACTCCCCGCCTACCCCTGCCCCCACTCCTGCCC
GCACAGCCCCGACCCATTTCCCCTCACCCAGTGACGTCCCCCCAGTTCTCGTTCTGTCCCCAAGATACCTATTTTTCTTC
AGACCATTCTTTCCAGTCAGATCAGTTCTTAAACTATTTCCATTCAGATGTCCCCTCATCTACCCAGACAGGATTTGACT
TCGAAGGTGACTTTATGTTTAGTCCCCAGCCGCCTAGGCCCTCCTTCCCCACACCTTATCAGCAGTGGGCCCCTGTGGTT
CATAGGGGTTTTCCCCGGAATCTACCTCGTGGCCCCTATGTGCCCTGGAGACGGCGACCCAAATCTCACAGGAAGCGGAC
CCCAGCCCTTCCAGAGCCGAGACCTCATTAG

Alignment

ORF - retro_pvam_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.99 %
• Parental protein coverage: 77.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAGGQLGEL
          MVH...SEV.QLLHNKFVV.LGDS.QR.VYKDLVLLLQKD.LLT..QLK.KGE.SFEQD.LV.GGQ....
Retrocopy MVHLLSSEVRQLLHNKFVVVLGDSVQRSVYKDLVLLLQKDCLLTHRQLKVKGEMSFEQDELVVGGQKSPM

Parental  HNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEGILEELTYGP-APDLVIINSCLWDLSRYGRCSMES
          HN.T.YREVRQ.CSG..HHLVRFYFLTRVY.EY..G.LEEL......PD.VIINSCLWD.SRYG..S..S
Retrocopy HNRTSYREVRQYCSG--HHLVRFYFLTRVYNEYVQGVLEELQADKHTPDVVIINSCLWDISRYGQDSVRS

Parental  YRENLERVFMRMDQVLPDSCLLVWNMAMPLGERVTGGFLLPELQPLAASLRRDVVEGNFYSATLAGDHYF
          YRENLE..F....QVLP.SCLLVWN.AMP.GE..TGGFLLPE.Q.LA..LR..V.E.NFYS...AG.H.F
Retrocopy YRENLENLFRHLGQVLPESCLLVWNTAMPVGEKITGGFLLPEQQSLALRLRLGVIEANFYSSAEAGKHGF

Parental  DVLDLHFHFRHAVRHRHWDGIHWDQHAHRHISHLLLTHVADAWGVELPKRNYPPDPWIEDWPEPNHLFQG
          DVLDLHFHFRHA..HR..DG.HW.Q.AHR..S.LLL.HVADAWGVELP.R..P...WI...........G
Retrocopy DVLDLHFHFRHAEKHRQGDGVHWNQYAHRQLSQLLLAHVADAWGVELPNRD-PVGKWIKAGRATGEPGLG

Parental  SQGQPPDFGEQLALPPPPPSPLPPPIP-FPYPLPQPSPPPLFPPLPQEAPFFPGQPFPPHEFFSYNPTED
          ...Q.........L.P.P..P.....P..P.P.P....PPL.P..P...P..P.....P...FS..P...
Retrocopy VERQAQASRDPQVLLPTPSLPPRRLRPLLPLPTPRLPLPPLLPAQPR--PISPHPVTSPQ--FSFCPQDT

Parental  FSMPPH
          .....H
Retrocopy YFSSDH

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_9 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343, retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163, retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333, retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9 ,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190, retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,