RetrogeneDB ID: retro_pvam_855

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_13667:16731..17841(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000016640
• Aliases: None
• Description: None

Sequence

>retro_pvam_855
TACCGCCAGGCCTCCCTGTACGTGGGCGACCTCCATGCGGAGGTCACCGAGGACCTGCTGTTCAAGAAGTTCAGCGCCGT
GGGGCCCGTGCTGTCCATCCGCATCTGCAGGGACCTGGTCACCCAGCGCTCGCTGGGCTACGCCTACGTGAACTTCCTGC
ACCTGGCCGATGCCCAGAAGGCCCTGGACACGATGAACTTCGACATGATCAAAGGCAAGTCCATCCGGCTCATGTGGTCC
CAGCGCGACGCTTACTTGAGGAAATCGGGCATCGGGAACGTGTTCATCAAGAACTTGCACAAGTCCATTGATAACAAAAC
GCTGTATGAGCACTTCTCGGCCTTCGGGAAGATCCTGTCCTCCAAGGTGATGAGTGACGACGCAGGCTCCCGGGGCTACG
CCTTCGTGCACTTCCAGAGCCAGACGGCCGCGGACCGCGCCATCGAGGCGATGAACGGGGCGCTGCTCAAGGGCTGTAGG
CTGTTCGTCGGCCCGTTCAAAAACCGCAAAGATCGGCAAGCTGAGCTCCAGAATAAAGCCAACGAATTCACCAATGTCTA
CATCAAAAACTTCGGAGACGACATGGACGATGAGAGACTGAAGGAGATTTTCAGCCATTTCGGCAAAATCCTGAGCGTTA
AGGTGATGACAGATTCCCGTGGGAGATCCAAAGGCTTTGGCTTCGTGAGTTTTGACAGCCATGAGGCTGCCCAGAGGGCT
GTTGAAATCATGAATGGGAAGGACTTGAGTGGACAGCCGCTTTTCGTAGGCCGGGCGCAAAAGAAAGCAGAGCGTCAGGC
CGAGTTAAAGCTAATGTTTGAGCAGATGAAACAGGAGAGATACCGGAGGTTCCGGGGCGTGAAGCTCTATATTAAGAACC
TGGATGACAGCATCGATGATGAACGTCTACGGAGAGAATTTTCTTCATTTGGATCAATTAGCAGAGTTAAGGTAATGAAG
GAAGAAGGACGAAGCAAAGGGTTTGGCTTGATCTGCTTCTCCTCTCCAGAGGAAGCCACTAAAGCAATGGTTGAGATGAA
TGGCCGTATTTTGGGCTCCAAGTCCCTCAACATTGCCCTGGCCCAGAGGCCCTAGGAGAGCACGACTCAC

Alignment

ORF - retro_pvam_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.65 %
• Parental protein coverage: 58.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
          Y..ASLYVGDLH..VTE..L..KFS..GP.LSIR.CRD..T.RSLGYAYVNF...ADA..ALDTMNFD.I
Retrocopy YRQASLYVGDLHAEVTEDLLFKKFSAVGPVLSIRICRDLVTQRSLGYAYVNFLHLADAQKALDTMNFDMI

Parental  KGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFET
          KGK..R.MWSQRD..LRKSG.GN.FIKNL.KSIDNK.LY..FSAFG.ILS.KV..D..GS.GY.FVHF..
Retrocopy KGKSIRLMWSQRDAYLRKSGIGNVFIKNLHKSIDNKTLYEHFSAFGKILSSKVMSDDAGSRGYAFVHFQS

Parental  QEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPA
          Q.AA.RAIE.MNG.LL.....FVG.FK.RK.R.AEL...A.EFTNVYIKNFG.DMDDERLK..F..FG..
Retrocopy QTAADRAIEAMNGALLKGCRLFVGPFKNRKDRQAELQNKANEFTNVYIKNFGDDMDDERLKEIFSHFGKI

Parental  LSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDR
          LSVKVMTD..G.SKGFGFVSF..HE.AQ.AV..MNGK.L.G....VGRAQKK.ERQ.ELK..FEQMKQ.R
Retrocopy LSVKVMTDSRGRSKGFGFVSFDSHEAAQRAVEIMNGKDLSGQPLFVGRAQKKAERQAELKLMFEQMKQER

Parental  ITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRI
          ..R..GV.LY.KNLDD.IDDERLR.EFS.FG.I...KVM.E.GRSKGFG..CFSSPEEATKA..EMNGRI
Retrocopy YRRFRGVKLYIKNLDDSIDDERLRREFSSFGSISRVKVMKEEGRSKGFGLICFSSPEEATKAMVEMNGRI

Parental  VATKPLYVALAQRKEERQAH
          ...K.L..ALAQR..E...H
Retrocopy LGSKSLNIALAQRP*ESTTH

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_855 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 15 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys	ENSNLEG00000003142	3 retrocopies	retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000007616	2 retrocopies	retro_pvam_1429, retro_pvam_695,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855 ,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,