RetrogeneDB ID: retro_pvam_723

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_971:162034..163082(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KARS
• Ensembl ID: ENSPVAG00000006746
• Aliases: None
• Description: lysyl-tRNA synthetase [Source:HGNC Symbol;Acc:6215]

Sequence

>retro_pvam_723
GGAAACACAACTGGGGTTCAGGGAAATCCTGGGGAAACCAAGAAGGGTGAGCTGAGCATCATTCCCTATGAGATCATTCT
GCTGTCTCCTTCCTTGCACATGTTACCTCACCTTCACTTTGGCCTCAAGGACAAGAAAACGTGATATCGTCAGAGGTACT
TGGTCTTGATCCTGAGTGACTTTGTGAGGCAGAAATTTATCATCTGCTCTAAGATCATCACATATGTAAGAAGTTTCTTA
GATGAGTTGGAATTCCTAGAGATTGAAACTCCCATGGTGAACATCGTCCCAGAGGGAGTTGTGGCCAAGCCTTTTATCAT
CTACCACAATGAGCTGGATATGAATTTATGTATGAGAATTGCTCCAGAATTCTACTCTGAGATGCTGGTGGTTGGTTGCA
TTGATCGGCATCCAATTTACAATATTGGACGCCAGTTCTAGAATGAAAAAAGTTGACTTGACTCACAATCTTGCGTTTAC
CACCTGTGAGTTCTACATGGCCTTTGTGGACAATCGTGATCTCATGGAAATGACAGAGATAATTTCAAGGATGGTGAAGT
ACATTACAGGCAGTTATAAGGTCACCTACCATCCAGATGGCTCGAAGGGCTAAATCTTTGGAATCGACTTCACCCCACCC
TTCCAGAGAATCGGCATGTAGAAGACCTTGAGATAGCCCTGGGGATGAAGCTGCCAGTAACCTCTTCGAAACAGAAGAAA
CTTACAAAATCCTCGATGATATCTGTGGCAAAAGCTATTGAATGCCCTCCACCTAAGACCACAGCCAGGCTCCTAGATAA
ACCTATTGGAGAATTCCTGAAAGTGACATACATTGATCCTACATTTATGTGTGATCATCTGCAGATAATGAGCCCTTTGG
CTAAATGGCACTGCTCTGAAAAGAGTTTAATAACTGAGTGCTTTGAGCTGTTTGCCATGAAGAAAAAAATATTCAATGCC
TACACTGAGCTAAATGATCCCCTGCAAATGGCAGCAGCTTTTTGAAGAACAAGCCAAGGCCCCTGGCATTGATTAGGCCA
TGTTCATT

Alignment

ORF - retro_pvam_723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.27 %
• Parental protein coverage: 56.25 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GDIIGVQGNPGKTKKGELSIIPHEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRS
          G...GVQGNPG.TKKGELSIIP.EI.LLSP.LHMLPHLHFGLKDK.T.YRQRYL.LIL.DFVRQKFII.S
Retrocopy GNTTGVQGNPGETKKGELSIIPYEIILLSPSLHMLPHLHFGLKDKKT*YRQRYLVLILSDFVRQKFIICS

Parental  KIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDR--VY
          KIITY.RSFLDEL.FLEIETPM.NI.P.G.VAKPFI.YHNELDMNL.MRIAPE.Y..MLVVG.IDR...Y
Retrocopy KIITYVRSFLDELEFLEIETPMVNIVPEGVVAKPFIIYHNELDMNLCMRIAPEFYSEMLVVGCIDRHPIY

Parental  EIGRQFRNE-GIDLTHNPEFTTCEFYMAYADYHDLMEITEKMISGMVKHITGSYKVTYHPDGPEGQAYEI
          .IGRQF.NE...DLTHN..FTTCEFYMA..D..DLME.TE..IS.MVK.ITGSYKVTYHPDG..G....I
Retrocopy NIGRQF*NE>KVDLTHNLAFTTCEFYMAFVDNRDLMEMTE-IISRMVKYITGSYKVTYHPDGSKG*IFGI

Parental  DFTPPFRRINM-VEELEKSLGVKLPDTKLFESEETRKILDDICVAKAVECPPPRTTARLLDKLVGEFLEV
          DFTPPF.RI.M.VE.LE..LG.KLP.T.......T......I.VAKA.ECPPP.TTARLLDK..GEFL.V
Retrocopy DFTPPFQRIGM<VEDLEIALGMKLPVTSSKQKKLTKSSM--ISVAKAIECPPPKTTARLLDKPIGEFLKV

Parental  TCINPTFICDHPQIMSPLAKWHRSKEGL-TERFELFVMKKEICNAYTELNDPMRQ-RQLFEEQAKAKAAG
          T.I.PTF.CDH.QIMSPLAKWH.S...L.TE.FELF.MKK.I.NAYTELNDP.....QLFEEQ..AKA.G
Retrocopy TYIDPTFMCDHLQIMSPLAKWHCSEKSLITECFELFAMKKKIFNAYTELNDPLQM>QQLFEEQ--AKAPG

Parental  DDEAMFI
          .D.AMFI
Retrocopy ID*AMFI

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_723 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013447	1 retrocopy	retro_chof_2324,
Callithrix jacchus	ENSCJAG00000014213	2 retrocopies	retro_cjac_4104, retro_cjac_608,
Homo sapiens	ENSG00000065427	1 retrocopy	retro_hsap_1191,
Gorilla gorilla	ENSGGOG00000005515	1 retrocopy	retro_ggor_930,
Mus musculus	ENSMUSG00000031948	8 retrocopies	retro_mmus_3536, retro_mmus_3537, retro_mmus_3538, retro_mmus_3539, retro_mmus_3540, retro_mmus_3541, retro_mmus_3542, retro_mmus_3543,
Nomascus leucogenys	ENSNLEG00000013072	1 retrocopy	retro_nleu_2080,
Pongo abelii	ENSPPYG00000007567	1 retrocopy	retro_pabe_992,
Pan troglodytes	ENSPTRG00000008364	1 retrocopy	retro_ptro_3036,
Pteropus vampyrus	ENSPVAG00000006746	2 retrocopies	retro_pvam_1301, retro_pvam_723 ,
Sorex araneus	ENSSARG00000011493	1 retrocopy	retro_sara_415,