RetrogeneDB ID: retro_ptro_3036

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392075.1:2969966..2971564(+)
• Located in intron of: ENSPTRG00000005820

Retrocopy information

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

Parental gene information

• Parental gene symbol: KARS
• Ensembl ID: ENSPTRG00000008364
• Aliases: None
• Description: Lysine--tRNA ligase [Source:UniProtKB/TrEMBL;Acc:H2QBJ2]

Sequence

>retro_ptro_3036
GTGGCAGTGGTACAGGGGGCTGAGGTGAAAGTGGATGGCAGCAAGCCAAAACTGAGCAAGAATGAGCTGAGGAGATCCCT
GAAAGCCAAGAAGAAAGTGGCAGAGAAGGAGGCCAAGCAGAAAGAACTCAGTGAGAAAGCTAAACCAGGCCACAGCTGCT
GTCACCAACCATACCACTGACAGTGGTGTGGGTACTGAGGAGAAGAGCCTGGACCCAAATCAACACTACAAGATCCACAG
TCAGGCAGTTTATCAACTGAATGTCAATGGGGAACACCCATACCCACACAAGTTCCATGCAGACATCTCATTCAATGACT
TCATCCAAGAATATAGTCACCAGCAGCCTGGGGGTCACCTGAATGATGTCACCTTAAAGGTGGCAGGTAGGATCCATGCT
AAAAGAGCTTCTGAGGGAAAGTTCATCTTCTATGACCTTCAAGGAGAGGGGGTCAAGTTGCAAGTCATGGTGAATCCCAG
AAATTATAAATCAGAAGAATTTATTCATATTAATAAGAAACTGCATCAAGGTGACATAATTGGAGTTCAGGGGAACCCTG
GGAAAACCAAGAAGGGTGAGCTAAGCATCATTTCTTATGAGATCACACTGCTGTCTCCCCGCATGCATATGTTACCTCAT
CTTCACTGTGGCCTCAAATACCAGGAAACAAGGTATCGTCAGAAATACTTGGACTTGATACTAAATGATTTTGTGAGGCA
GAAATTTATCATCTGCTCTAAGATCATCACATGTATAAGAAGTTTCTTGGATGAACTGGGATTCCTAAAGATTGAAACTC
CCATGGTGAACATCATCCCAGGGGGAGCTGTGGCCAAGCTTTTCATCACTTATGACAATGAGCTGGACATGAGAATTGCT
CCGGAACTCTATCATAAGATGCTAGTGGTTGGTGGCACCAAGCAGATTTATGAAACTGGATGCCATTTCCAGAATGAAGG
GATTGATTTGAGGCACAATCCTGAGTTCACCACCTGTGAGTTCTATATGGCCTATGCAGACTACCATAATCTCTTGGAAA
TCACAGAGAAGATGGTTTCAGGGATGGTAAAGCATATTACAGGCAGTTACAAGGTCAGCTACCACCCAGATGGCCCATAG
GGCCAGGCCTATGATACTGACTTCACCCCACCCTTCCAGAGAATCAGCATGGTAGAAGAACTTGAGAAAGCCCTGGGGGT
AAAGCTGCCAGAAACTAACCTCTTTGAAACTGATGAAACTTGCAAACTTCTTAATGATATCTGTGTGGCAAAAGCTGTTG
AATGCCCTCTACCTTGGACCACAGCCAAGCTCCTTGACAAGCTTGTAGGGGAGTTCCTGGAAATGATTTGCATCAATCCT
ACATTAATCTGTGATCATCCACAGATAATGAGCGCTATGGCAAATGGCACTGCTCTGAAGAGAATCTGTCCAAGCACTTT
GAGCTGCTTGTCATGAAGAAAGAGATAAGCGATGCCTAAACTAAGCTGAATGATCCTGTGCCACAGCAGCGGGTTTTTGA
ACAACAGGCCAAAGCCAAGGCCACAGGTCATGATGAGGCCATTTCATAGATGAAAACTTCTGTACCGCCCTGGAATAC

Alignment

ORF - retro_ptro_3036 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.86 %
• Parental protein coverage: 90.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAVQAAEVKVDGSEPKLSKNELKRRLKAE-KKVAEKEAKQKELSEKQLSQATAAATNHTTDNGVGPEEE
          .A.VQ.AEVKVDGS.PKLSKNEL.R.LKA...K........K..S...L.QATAA.TNHTTD.GVG.EE.
Retrocopy VAVVQGAEVKVDGSKPKLSKNELRRSLKAK>RKWQRRRPSRKN-SVRKLNQATAAVTNHTTDSGVGTEEK

Parental  SVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASG
          S.DPNQ.YKI.SQA..QL.VNGE.PYPHKFH.DIS..DFIQ.YSH.QPG.HL.D.TLKVAGRIHAKRAS.
Retrocopy SLDPNQHYKIHSQAVYQLNVNGEHPYPHKFHADISFNDFIQEYSHQQPGGHLNDVTLKVAGRIHAKRASE

Parental  GKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPC
          GK.IFYDL.GEGVKLQVM.N.RNYKSEE.FIHIN.KL..GDIIGVQGNPGKTKKGELSII.YEITLLSP.
Retrocopy GKFIFYDLQGEGVKLQVMVNPRNYKSEE-FIHINKKLHQGDIIGVQGNPGKTKKGELSIISYEITLLSPR

Parental  LHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAV
          .HMLPHLH.GLK..ETRYRQ.YLDLILNDFVRQKFII.SKIIT.IRSFLDELGFL.IETPM.NIIPGGAV
Retrocopy MHMLPHLHCGLKYQETRYRQKYLDLILNDFVRQKFIICSKIITCIRSFLDELGFLKIETPMVNIIPGGAV

Parental  AKPFITYHNELDMNLYMRVAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHD
          AK.FITY.NELD....MR.APELYHKMLVVGG....YE.G..F.NEGIDL.HNPEFTTCEFYMAYADYH.
Retrocopy AKLFITYDNELD----MRIAPELYHKMLVVGGTKQIYETGCHFQNEGIDLRHNPEFTTCEFYMAYADYHN

Parental  LMEITEKMVSGMVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEET
          L.EITEKMVSGMVKHITGSYKV.YHPDGP.GQAYD.DFTPPF.RI.MVEELEKALG.KLPETNLFET.ET
Retrocopy LLEITEKMVSGMVKHITGSYKVSYHPDGP*GQAYDTDFTPPFQRISMVEELEKALGVKLPETNLFETDET

Parental  RKILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLA-KWHRSKEGLTERFEL
          .K.L.DICVAKAVECP.P.TTA.LLDKLVGEFLE..CINPT.ICDHPQIMS..A.KWH.S.E.L...FEL
Retrocopy CKLLNDICVAKAVECPLPWTTAKLLDKLVGEFLEMICINPTLICDHPQIMSAMA<KWHCSEENLSKHFEL

Parental  FVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAM-FIDENFCTALEY
          .VMKKEI..A.T.LNDP..Q...FE.QAKAKA.G.DEA..FIDENFCTALEY
Retrocopy LVMKKEISDA*TKLNDPVPQQRVFEQQAKAKATGHDEAI<FIDENFCTALEY

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.05 RPM	54.05 RPM
SRP007412_cerebellum	0.07 RPM	85.10 RPM
SRP007412_heart	0.00 RPM	81.81 RPM
SRP007412_kidney	0.00 RPM	106.46 RPM
SRP007412_liver	0.00 RPM	97.58 RPM
SRP007412_testis	0.00 RPM	195.17 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3036 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3036 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3036 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1191
Gorilla gorilla	retro_ggor_930
Pongo abelii	retro_pabe_992

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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,