RetrogeneDB ID: retro_nleu_2080

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397327.1:2622306..2623907(+)
• Located in intron of: ENSNLEG00000001302

Retrocopy information

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

Parental gene information

• Parental gene symbol: KARS
• Ensembl ID: ENSNLEG00000013072
• Aliases: None
• Description: lysyl-tRNA synthetase [Source:HGNC Symbol;Acc:6215]

Sequence

>retro_nleu_2080
GTGGCAGTGGTACAGGGGGCTGAGGTGAAAGTGGATGGCAGCAAGCCAAAACTGAGGAAGAATGAGTTGAAGAGATCCCT
GAAAGCCAAGAAGAAAGTGGCAGAGAAGGAGGCCAAGCAGAAAGAACTCAGTGAGAAATAGCTAAACCAGGCCACAGCTG
CTGTCACAAACCATACCACTGACAGTGGTGTGGGTACTGAGGAGAAGAGCCTGGACCCAAATCAACACTACAAGATCCAC
AGTCAGGCAGTTTATCAACTGAATGTCAATGGGGAACACCTATACCCACACAAGTTCCATGCAGACATCTCACTCAATGA
CTTCATCTAAGAATATAGTCACCAGCAGCCTGGGGGTCACCTGAATGATGTTACCTTAAAGGTGGCAGGTAGGATCCATG
CTAAAAGAGCTTCTGAGGGAAAGTTCATCTTCTATGACCTTCAAGGAGAGGGGGTCAAGTTGCAAGTCATGGCAAATCCC
AGAAATTATAAATCAGAAGAATTTATGCATATTAATAACAAACTGCATCAAGGAGACGTAATTGGAGTTCAGGGGAACCC
TGGGAAAACCAAGAAGGGTGAGCTGAGCATCATTCCTTATGACATCACACTGCTGTCTCCCCACTTGCATATGTTACCTC
ATCTTCACTGTGGCCTCAAAGACCAGGAAACAAGGTATCGTCAGAAATACTTGGACTTGATACTAAATGATTTTGTGAGG
CAGAAATTTATCATCTGCTCTAAGATCATCACATGTATAAGAAGTTTCTTGGATGAACTGGGATTCCTATAGATTGAAAC
TCCCATGATGAACATCATCCCAGGGGGAGCTGTGGCCAAGCTTTTCATCACTTATGACAATGAGCTGGACATGAGAATCG
CTCCAGAACTCTATCATAAGATGCTAGTGGTTGGTGGCACCAAGCAGATTTATGAAACTGGATGCCAGTTTCAGAATGAA
GGGATTGATTTGAGGCACAATCCTGAATTCACCACTTGTGAGTTCTACATGGCCTATGCAGACTACCACAATCTCTTGGA
AATCACAGAGAAGATGGTTTCAGGGATGGTGAAGCATATTATAGGCAGTTGCAAGGTCAGCTACCACCCAGATGGCCCAC
AGGGCCAGGTCTATGATACTGACTTCACCCAACCCTTCCAGAGAATCAGCATGGTAGAAGAACTTGAGAAAGCCCTGGGG
GTAAAGCTGCCAGAAACTAACCTCTTTGAAACTGATGAAACTTGCAAACTTCTTAATGATATCCGTGTGGCAAAAGCTGT
TGAATGCCCTCTACCTTGGACCACAGCCAGGCTCCTTGACAAGCTTGTAGGGGAGTTCCTGGAAGTGATTTGCATCAATC
CTACATTAATCTGTGATCATCCCCAGATAATGAGCGCTATGGCAAATGGCACCGCTCTAAAGGGAATCTGTCCAAGCACT
TTGAGCTGCTTGTCATGAAGAAAGAGATATGCGATGCCTAAACTAAGCTGGAATGATCCTGTGCCACAGCAGCGGGTTTT
TGAAGAACAGGCCAAAGCCAAGGCCACAGGTGATGATGAGGCCATTTCATAGATGAAAACTTCTGTACCGCCCTGGAATA
T

Alignment

ORF - retro_nleu_2080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.37 %
• Parental protein coverage: 90.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAVQAAEVKVDGSEPKLSKNELKRRLKAEKKVAEKEAKQKELSEKQLSQATAAATNHTTDNGVGPEEES
          .A.VQ.AEVKVDGS.PKL.KNELKR.LKA.KKVAEKEAKQKELSEK.L.QATAA.TNHTTD.GVG.EE.S
Retrocopy VAVVQGAEVKVDGSKPKLRKNELKRSLKAKKKVAEKEAKQKELSEK*LNQATAAVTNHTTDSGVGTEEKS

Parental  VDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASGG
          .DPNQ.YKI.SQA..QL.VNGE..YPHKFH.DISL.DFI..YSH.QPG.HL.D.TLKVAGRIHAKRAS.G
Retrocopy LDPNQHYKIHSQAVYQLNVNGEHLYPHKFHADISLNDFI*EYSHQQPGGHLNDVTLKVAGRIHAKRASEG

Parental  KLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCL
          K.IFYDL.GEGVKLQVMAN.RNYKSEE.F.HINNKL..GD.IGVQGNPGKTKKGELSIIPY.ITLLSP.L
Retrocopy KFIFYDLQGEGVKLQVMANPRNYKSEE-FMHINNKLHQGDVIGVQGNPGKTKKGELSIIPYDITLLSPHL

Parental  HMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVA
          HMLPHLH.GLKD.ETRYRQ.YLDLILNDFVRQKFII.SKIIT.IRSFLDELGFL.IETPMMNIIPGGAVA
Retrocopy HMLPHLHCGLKDQETRYRQKYLDLILNDFVRQKFIICSKIITCIRSFLDELGFL*IETPMMNIIPGGAVA

Parental  KPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDL
          K.FITY.NELD....MRIAPELYHKMLVVGG....YE.G.QF.NEGIDL.HNPEFTTCEFYMAYADYH.L
Retrocopy KLFITYDNELD----MRIAPELYHKMLVVGGTKQIYETGCQFQNEGIDLRHNPEFTTCEFYMAYADYHNL

Parental  MEITEKMVSGMVKHITGSYKVTYHPDGPEGQAYDIDFTPPFQRINMVEELEKALGMKLPETNLFETEETR
          .EITEKMVSGMVKHI.GS.KV.YHPDGP.GQ.YD.DFT.PFQRI.MVEELEKALG.KLPETNLFET.ET.
Retrocopy LEITEKMVSGMVKHIIGSCKVSYHPDGPQGQVYDTDFTQPFQRISMVEELEKALGVKLPETNLFETDETC

Parental  KILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLA-KWHRSKEGLTERFELF
          K.L.DI.VAKAVECP.P.TTARLLDKLVGEFLEV.CINPT.ICDHPQIMS..A.KWHRSK..L...FEL.
Retrocopy KLLNDIRVAKAVECPLPWTTARLLDKLVGEFLEVICINPTLICDHPQIMSAMA<KWHRSKGNLSKHFELL

Parental  VMKKEICNAYTEL-NDPMQQRQLFEEQAKAKAAGDDEAM-FIDENFCTALEY
          VMKKEIC.A.T.L.NDP..Q...FEEQAKAKA.GDDEA..FIDENFCTALEY
Retrocopy VMKKEICDA*TKL>NDPVPQQRVFEEQAKAKATGDDEAI<FIDENFCTALEY

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2080 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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,