RetrogeneDB ID: retro_pvam_173

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1741:88103..89639(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LPCAT2
• Ensembl ID: ENSPVAG00000007801
• Aliases: None
• Description: lysophosphatidylcholine acyltransferase 2 [Source:HGNC Symbol;Acc:26032]

Sequence

>retro_pvam_173
AGGAGGAAGTCCCTGTATCCGCCAGCAGTGGCCAACCCTTTCGTGCAGCAGACGAACATCAGCGCGTGGCGCTGGGCCTC
CATCATTCTCGCGGGGTCTGTGCTGGTCCCGGTGCGGGTGACCTGCATTGCCTTCCTCCTCATCTTCCTCTGGCCGATGG
CCGCACTTTCCACCATAGGCGGTTCTGCTCATCCAGCCAAACCCGCCACGAGTTGGAGGAGAAAACTGGCAAAACCGGCT
CTCAAATTCTTGTATCAGGCAATATTCTTTTTAGCAGGGTTCCTTGTTAAAGTGAAAGGGAAAAAGGCAACCCGAGAAGA
GGCCCCCATCTTTGTCACAGCACCGCACTCCACTTTCTTTGACGCAATCGCCTGTGTTGTGGCAGGGTTACCCTCCGTAG
TCTCTGCAAGTAAAAACGCACATATCCCAGTGGCTGGAAAATTCCTACTGTCAACACAGCCGGTGCTTGTTACCCGAGAG
GACCCCAATTCCAGGAAGACAACCCGGGAAGAAATTCTGAAGCGAGTGACATCCAAAAGAAAGTGGCCACAGATCCTGAT
TTTCCCAGAAGGAGTGTGTACCAATCGCACGTGTCTGATCACTTTTAAACTAGGGGCCTTTTCTCCAGGTGTTCCTGTAC
AGCCAGTGCTACTCAGGTACCCAAATGCCCTGGACACAGTGACCTGGACCTGGCAGGGGTTTACAGGCTTCCAGGCTTGT
ATGTTGACCCTGAGTCAACTCTTCACCAGAGTAGAAGTTGAGTTTATGCCTGTTTACATCCCAAATGACGAAGAAAAGAA
AAACCCCATCCTTTTTGCCAATACAGTGAGGATCAACATGGCAAATGCTCTGGGGTTACCTGTGACAGACCACACTTATG
AAGACTGCAGATTGATGATTACCGCAGGTAACCTTCGACTACCCATGGAAACTGGCTTGGTGGAATTTACAAAAATTAGC
AAGAAATTAAAGTTAGATTGGGATAATATTCACCAGCATTTGGATGAATATGCTGCAATTGCAGTTGCCTCAAAGGGAGG
GAAGATAGGAATTGAAGAATTTGCAAATTATTTAAAACTCCCAATTTCAGAGCCCTTGAGACAAATTTTTGCCCTTTTTG
ACAGGAATAATGATGGCAACATAGACTTCAGAGAGTATGTGATAGGTCTGACTGTCCTATGTAATCCTGCCAACACTAAA
AAGATTCTGCAGATGTCATTTAAGCTTTTTGATCTTGATAAGGATGGTTTCATAACAAAACAGGAGTTAGCTACTGTACT
TCAGGCGGCTTTTGGAGTGCCAGATCTTGATGTTTCCAGACTCTTTCGGGAAATAGCTGGACAGAAATCAGAGTACATTT
CATACAAGAAATTTAAGAAATTTGCCTTGAAGCATCCAGAATATGCCAAGTTATTTCATTCATTCTTAGACCTACAGGCA
GCCTATATCTATGCATTACCAAAAGTGCAGGTTTAATCGCTGTGTTCAGATGTTAAAGACAGCCCTGAAAATGGTGAAAA
TACCTTCCTGGGAGAA

Alignment

ORF - retro_pvam_173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.4 %
• Parental protein coverage: 93.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQASFFPPPVPNPFVQQTRMGAAKRIQIFLLGIILLPIRALLVAIILLLAWPFAAVSTACCPEKMTHPVT
          R..S..PP.V.NPFVQQT...A.....I.L.G..L.P.R....A..L...WP.AA.ST.........P.T
Retrocopy RRKSLYPPAVANPFVQQTNISAWRWASIILAGSVLVPVRVTCIAFLLIFLWPMAALSTIGGSAHPAKPAT

Parental  GWRRTITQRILKFLGHAMFLSMGFIVTVKGRIASPVEAPIFVVAPHSTFFDGIACVVTGLPSIVSRLENV
          .WRR......LKFL..A.F...GF.V.VKG..A...EAPIFV.APHSTFFD.IACVV.GLPS.VS...N.
Retrocopy SWRRKLAKPALKFLYQAIFFLAGFLVKVKGKKATREEAPIFVTAPHSTFFDAIACVVAGLPSVVSASKNA

Parental  QVPLIGRLLRAVQPVLVSRVDPDSRKNTINEIVRRATSGGEWPQILVFPEGTCTNRSCLITFKPGAFIPG
          ..P..G..L...QPVLV.R.DP.SRK.T..EI..R.TS...WPQIL.FPEG.CTNR.CLITFK.GAF.PG
Retrocopy HIPVAGKFLLSTQPVLVTREDPNSRKTTREEILKRVTSKRKWPQILIFPEGVCTNRTCLITFKLGAFSPG

Parental  VPVQPVLLRYPNKLDTVTWTWQGYTFLQLVVLTCCQPFTKVEVEFMPIQAPNDEEKHDPVLFASRVRNLM
          VPVQPVLLRYPN.LDTVTWTWQG.T..Q...LT..Q.FT.VEVEFMP...PNDEEK..P.LFA..VR..M
Retrocopy VPVQPVLLRYPNALDTVTWTWQGFTGFQACMLTLSQLFTRVEVEFMPVYIPNDEEKKNPILFANTVRINM

Parental  AEALRIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFTKISRKLKLDWDGVRKHLSEYAAIASSTKGGRIG
          A.AL..PVTDHTYEDCRLMI.AG.L.LPME.GLVEFTKIS.KLKLDWD....HL.EYAAIA...KGG.IG
Retrocopy ANALGLPVTDHTYEDCRLMITAGNLRLPMETGLVEFTKISKKLKLDWDNIHQHLDEYAAIAVASKGGKIG

Parental  IEEFAEYLKLPVSDVLRQLFALFDRNHDGSIDFREYVIGLAVLCNPANTEEIIQVAFKLFDVDEDGYISE
          IEEFA.YLKLP.S..LRQ.FALFDRN.DG.IDFREYVIGL.VLCNPANT..I.Q..FKLFD.D.DG.I..
Retrocopy IEEFANYLKLPISEPLRQIFALFDRNNDGNIDFREYVIGLTVLCNPANTKKILQMSFKLFDLDKDGFITK

Parental  DEFSTIMQASLGVPDLDVSGLFKEIA--QGDSVSYEEFKSFALKHPEYAKIFTAYLDLQASHVFSLPEEG
          .E..T..QA..GVPDLDVS.LF.EIA.......SY..FK.FALKHPEYAK.F...LDLQA.....LP...
Retrocopy QELATVLQAAFGVPDLDVSRLFREIAGQKSEYISYKKFKKFALKHPEYAKLFHSFLDLQAAYIYALPKV-

Parental  QTAPAVASNKVSPESHEESASGK
          Q........K.SPE..E....G.
Retrocopy QV*SLCSDVKDSPENGENTFLGE

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_173 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 20 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019272	1 retrocopy	retro_btau_64,
Callithrix jacchus	ENSCJAG00000012902	1 retrocopy	retro_cjac_2945,
Dasypus novemcinctus	ENSDNOG00000006859	1 retrocopy	retro_dnov_1735,
Dipodomys ordii	ENSDORG00000013193	1 retrocopy	retro_dord_399,
Equus caballus	ENSECAG00000009649	1 retrocopy	retro_ecab_865,
Erinaceus europaeus	ENSEEUG00000014277	1 retrocopy	retro_eeur_109,
Homo sapiens	ENSG00000087253	1 retrocopy	retro_hsap_185,
Gorilla gorilla	ENSGGOG00000005144	1 retrocopy	retro_ggor_266,
Loxodonta africana	ENSLAFG00000003965	1 retrocopy	retro_lafr_66,
Myotis lucifugus	ENSMLUG00000004008	1 retrocopy	retro_mluc_88,
Macaca mulatta	ENSMMUG00000004478	1 retrocopy	retro_mmul_392,
Mus musculus	ENSMUSG00000033192	1 retrocopy	retro_mmus_270,
Nomascus leucogenys	ENSNLEG00000001258	1 retrocopy	retro_nleu_994,
Pongo abelii	ENSPPYG00000007358	1 retrocopy	retro_pabe_445,
Pan troglodytes	ENSPTRG00000008124	2 retrocopies	retro_ptro_171, retro_ptro_2928,
Pteropus vampyrus	ENSPVAG00000007801	1 retrocopy	retro_pvam_173 ,
Rattus norvegicus	ENSRNOG00000016643	1 retrocopy	retro_rnor_309,
Sorex araneus	ENSSARG00000011914	1 retrocopy	retro_sara_88,
Sarcophilus harrisii	ENSSHAG00000012383	1 retrocopy	retro_shar_116,
Tursiops truncatus	ENSTTRG00000001182	1 retrocopy	retro_ttru_188,