RetrogeneDB ID: retro_pvam_1301

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_5796:1..1225(-)
• 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_1301
AAAAATGAGCTAAAGAAATGCCTGAAAGCTGAGAAGAAGGTAGTAGAGAAGTAGGCCCAAGCAGAAGGAGCTCAGTGAGA
AACAAACTAAGCTAAGCCAATGCTGCTGCCACCAACTACACCAATAACAGCAACGTCGGTGCCCAGTTAGAGAGCCTGGA
CCCAAACCAATACTACAAGATCCTCAGTCAATCGGCCCACCAACTAAAGGTTAATGACTGGTACCCATCCAGATTCCATA
TAGACATCTCACTCACTCGCTTCATCCAAGAATAAAGTCACATGTAACCTGGGGACCACCCAAGTAACAGCATCTTAAAG
GTGGCAGGTAGGATCCATGCCAAAAGAGCTTCTGGGGGAAAGTTCATCTTCTATGGTTTTCGAGGAGAGGGCGCCAATTT
GCAAGTCATGACCAATTCCAGGAATTATAAATCAGAAGAAGAATTTATTCCTATCAATAACAAACTACATTGGGGAGACA
TAATTGAATTCAGGGGAATCTTTGGAAAACCAAGAAGGGTGAGCTAAGCATCATTCCCTATGAGAATACACCGAGAACTC
CTTGCTTGCATATGTTACCTCATCCTCACTTTGGCCTCAAAGACAAGGGAACACAATATCGTCAGGGATACTAGGAGTTG
TTTCTGAATGACTTTGTGAGGCAGAAATTTATCATTCACTCAAAGATCATCGCATATGTAAGAAATTTTTGGATGAGTTG
GGATTCCTAGAGCTTGAAACTCCCATGATGAACATCATCCCAGAGGGAGCTGTGGCCAAGCCTTGTATCACTTACCACAA
TGAGCTGGACAAGAATTTATATATGTGAATTGCTCTGAACTCTACCATGAGATGCTGGTAGTTGGGGGCATTGACCAGGT
TTATGAAACTGGACACCAGTTCTGGAATGAAGGAACTGATTTGACTCACAATCCTGAAGCACTATAGCCTATGTTCTACA
TGGCCTATGCAAAATACCATGATCTCATGGAAATCACGGAGAAAATGATTTCAGGGATGGTGAAGCACATTACAGGCAGT
AAAAAGGTCACCTACTACCCAGATGACCCAAAGGGCCAAGTCTATGAGATTGACTTTACCCCACCCTTCTAAAGAATCAG
AGTAGAAGAGCTTGAGAAAGCCCTGGGAGTGATGCTGCTAGAAACTAACCTTAAAGGAAACTGAAGAAACTCACAAAATT
CTTAATACCTGTATGGCAAAAGCC

Alignment

ORF - retro_pvam_1301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.64 %
• Parental protein coverage: 66.03 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RSELKRRLKAEKKVAEKEA-KQKELSEKQ-LSQANAAATNHTNDNDVGAEEESLDPNQYYKIRSQAVHQL
          ..ELK..LKAEKKV.EK.A.KQKELSEKQ.LS.ANAAATN.TN...VGA..ESLDPNQYYKI.SQ..HQL
Retrocopy KNELKKCLKAEKKVVEK*A>KQKELSEKQ>LS*ANAAATNYTNNSNVGAQLESLDPNQYYKILSQSAHQL

Parental  KISGEDPYPHKFHVDVSLTHFIQEYSHLQPGDHLSDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVM
          K....D.YP..FH.D.SLT.FIQE.SH..PGDH.S...LKVAGRIHAKRASGGK.IFY..RGEG..LQVM
Retrocopy KVN--DWYPSRFHIDISLTRFIQE*SHM*PGDHPSNSILKVAGRIHAKRASGGKFIFYGFRGEGANLQVM

Parental  ANSRNYKSEEEFIRINNKLRRGDIIG-VQGNPGKTKKGELSIIPHEITLLSPCLHMLPHLHFGLKDKETR
          .NSRNYKSEEEFI.INNKL..GDII...QGN..KTKKGELSIIP.E.T...PCLHMLPH.HFGLKDK.T.
Retrocopy TNSRNYKSEEEFIPINNKLHWGDIIE<IQGNLWKTKKGELSIIPYENTPRTPCLHMLPHPHFGLKDKGTQ

Parental  YRQRYLDLILNDFVRQKFIIRSKIITYIRSF-LDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLY
          YRQ.Y..L.LNDFVRQKFII.SKII.Y.R.F.LDELGFLE.ETPMMNIIP.GAVAKP.ITYHNELD.NLY
Retrocopy YRQGY*ELFLNDFVRQKFIIHSKIIAYVRNF<LDELGFLELETPMMNIIPEGAVAKPCITYHNELDKNLY

Parental  MRIA-PELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMISGMVKH
          M.IA..ELYH.MLVVGGID.VYE.G.QF.NEG.DLTHNPE.....FYMAYA.YHDLMEITEKMISGMVKH
Retrocopy M*IA<SELYHEMLVVGGIDQVYETGHQFWNEGTDLTHNPEAL*PMFYMAYAKYHDLMEITEKMISGMVKH

Parental  ITGSYKVTYHPDGPEGQAYEIDFTPPFRRINMVEELEKSLGVKLPDTK-LFESEETRKILDDICVAKA
          ITGS.KVTY.PD.P.GQ.YEIDFTPPF.RI..VEELEK.LGV.L..T..L.E.EET.KIL...C.AKA
Retrocopy ITGSKKVTYYPDDPKGQVYEIDFTPPF*RIR-VEELEKALGVMLLETN>LKETEETHKIL-NTCMAKA

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_1301 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 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,