RetrogeneDB ID: retro_pabe_992

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:41891252..41892791(+)
• Located in intron of: ENSPPYG00000005317

Retrocopy information

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

Parental gene information

• Parental gene symbol: KARS
• Ensembl ID: ENSPPYG00000007567
• Aliases: None
• Description: lysine--tRNA ligase [Source:RefSeq peptide;Acc:NP_001127155]

Sequence

>retro_pabe_992
AAGAATGAGCTGAAGAGATCCCTGAAAGCCAAGAAGGAAGTGGCACAGGAGGAGGCCAAGCAGAAAGAACTCAGTGAGAA
ATAGCTAAACCAGGCCACAGCTGCTGTCACCAACCATACCACTGACAGTGGTGTGGGTACTGAGGAGAAGAGCTTTGACC
CAAATCAATACTACAAGATCCACAGTCAGGCAGTTTATCAACTGAATGTCAATGGGGAACACCCATACCCACACAAGTTC
CATGCAGACATCTCACTCAATGACTTCATCCAAGAATATAGTCACTAGCAGCCTGGGGGTCACCTGAATGATGTCACCTT
AAAGGTTGCAGGTAGGATCCATGCTAAAAGAGCTTCTGAGGGAAAGTTCATCTTCTATGACCTTCAAGGAGAGGGGGTCA
AGTTGCAAGTCATGGTGAATCCCAGAAATTATAAATCATTAGAATTTATTCATATTAATAACAAACTGCATCAAGGAGAC
ATAATTAGTTCAGGGGAACCCCGGGAAAACCAAGAAGGGTGAGCTGAGCATCATTCCTTATGAGATCACACTGCTGTCTC
CCCGCATGCATATGTTACCTCATCTTCACTGTGGCCTCAAAGACCAGGAAACCAGGTATCGTCAGAAATACTTGGACTTG
ATACTAAATGATTTTGTGAAGCAGAAATTTATCATCTGCTCTAAGACCATCACACGTATAAGAAGTTTCTTGGATGAACT
GGGATTCCTAGAGATTGAAACTCCCATGATGAATATCATCCCAGGGGGAGTTGTGGCCAAGCTTTTCATCACTTATGACA
ATGAGCTGGACATGAGAATTGCTCCAGAACTCTATCATAGGATGCTAGTGGTTGGTGGCACCAAGCAGATTTATGAAACT
GGACGCCAGTTCCAGAATGAAGGGATTGATTTGAGGCACAATCCTGAGTTCACCACCTGTGAGTTCTACATGGCCTATGC
AGACTACTACAATCTCTTGGAAATCACAGAGAAGATGGTTTCAGGGATGGTAAAGCATATTACAGGCAGTTACAAGGTCA
GCTACCACCCAGATGGCCCATAGGGCCAGGCCTATGATAACTGACTTCACCCCACCCTTCCAGAGAATCAGCATGGTAGA
ACTTGAGAAAGCCCTGGGGGTAAAGCTGCCAGAAACTAACCTCTTTGAAACTGATGAAACTTGCAAACTTCTTAATGATA
TCTGTGTGGCAAAAGCTGTTGAATGCCCTCTACCTTGGACCACAGCCAGGCTCCTTGACAAGCTTGTAGGGGAGTTCCTG
GAAGTGATTTGCATCAATCCTACATTAATCTGTGATCATCCACAGATAATGAGCACTATGGCAAATGGCACTGCTCTAAA
GAGAATCTGTCCAAGCACTCTGAGCTGCTTGTCATGAAGAAAGAGATATGCGATGCCTAAACTAAGCTGAATGATCCTGT
GCCACAGCAGCGGGTTTTTGAAGAACAGGCCAAAGCCAAGGCCACAGGTGAGGATGAGGCTATTTCATAGATGAAAACTT
CTGTACCGCCCTGGAATAC

Alignment

ORF - retro_pabe_992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.77 %
• Parental protein coverage: 83.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RSELKRRLKAEKKVAEKEAKQKELSEKQLSQATAAATNHTTDNGVGPEEESLDPNQYYKIRSQAVHQLKV
          ..ELKR.LKA.K.VA..EAKQKELSEK.L.QATAA.TNHTTD.GVG.EE.S.DPNQYYKI.SQAV.QL.V
Retrocopy KNELKRSLKAKKEVAQEEAKQKELSEK*LNQATAAVTNHTTDSGVGTEEKSFDPNQYYKIHSQAVYQLNV

Parental  NGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMAN
          NGE.PYPHKFH.DISL.DFIQ.YSH.QPG.HL.D.TLKVAGRIHAKRAS.GK.IFYDL.GEGVKLQVM.N
Retrocopy NGEHPYPHKFHADISLNDFIQEYSH*QPGGHLNDVTLKVAGRIHAKRASEGKFIFYDLQGEGVKLQVMVN

Parental  SRNYKSEEEFIHINNKLRRGDIIGVQGNP-GKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYR
          .RNYKS..EFIHINNKL..GDII...G.P.GKTKKGELSIIPYEITLLSP..HMLPHLH.GLKD.ETRYR
Retrocopy PRNYKS-LEFIHINNKLHQGDIIS-SGEP>GKTKKGELSIIPYEITLLSPRMHMLPHLHCGLKDQETRYR

Parental  QRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRI
          Q.YLDLILNDFV.QKFII.SK.IT.IRSFLDELGFLEIETPMMNIIPGG.VAK.FITY.NELDM....RI
Retrocopy QKYLDLILNDFVKQKFIICSKTITRIRSFLDELGFLEIETPMMNIIPGGVVAKLFITYDNELDM----RI

Parental  APELYHKILVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHVTGS
          APELYH..LVVGG....YE.GRQF.NEGIDL.HNPEFTTCEFYMAYADY..L.EITEKMVSGMVKH.TGS
Retrocopy APELYHRMLVVGGTKQIYETGRQFQNEGIDLRHNPEFTTCEFYMAYADYYNLLEITEKMVSGMVKHITGS

Parental  YKVTYHPDGPEGQAYD-VDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICVAKAVECPPP
          YKV.YHPDGP.GQAYD..DFTPPF.RI.MV.ELEKALG.KLPETNLFET.ET.K.L.DICVAKAVECP.P
Retrocopy YKVSYHPDGP*GQAYD>TDFTPPFQRISMV-ELEKALGVKLPETNLFETDETCKLLNDICVAKAVECPLP

Parental  RTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLA-KWHRSKEGLTERFELFVMKKEICNAYTELNDPM
          .TTARLLDKLVGEFLEV.CINPT.ICDHPQIMS..A.KWH.SKE.L....EL.VMKKEIC.A.T.LNDP.
Retrocopy WTTARLLDKLVGEFLEVICINPTLICDHPQIMSTMA<KWHCSKENLSKHSELLVMKKEICDA*TKLNDPV

Parental  RQRQLFEEQAKAKAAGDDEAM-FIDENFCTALEY
          .Q...FEEQAKAKA.G.DEA..FIDENFCTALEY
Retrocopy PQQRVFEEQAKAKATGEDEAI<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	0.00 RPM	53.47 RPM
SRP007412_cerebellum	0.49 RPM	52.90 RPM
SRP007412_heart	0.00 RPM	56.17 RPM
SRP007412_kidney	0.03 RPM	68.61 RPM
SRP007412_liver	0.03 RPM	56.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_992 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_992 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_992 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1191
Pan troglodytes	retro_ptro_3036
Gorilla gorilla	retro_ggor_930

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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,