RetrogeneDB ID: retro_pabe_1760

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:16307958..16309063(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000006153
• Aliases: None
• Description: None

Sequence

>retro_pabe_1760
AAAAAGAATCATCATCAAATTGTGTGTACAGAGTTTTCATCATGGATAGCTGTGAGGAGCTATCCTGCCGTATCTGAACT
TCATTGGAAAGGTGGTGGACTCAAAGGATCTCTGTCTAAATATTTCCCATGAGATGTTGCAACAAAGCAAAATTTTGAAA
GTTATCAGGAAGAATTTGGTCAAAAAATGCTTAGAACTCTTTACCAAACTGGCAGAAGATAAAGAGAACTACAAGAAGTT
CTATAAGCAGTTCTCTAAAAGCATAAAGCTTGAAATATACAAAGACTCTCAACATTGGAAGAAGTTTTCAGAGCTATTAA
GATACTACACATCTGCTTCTGGTTGATGAGATGGTTTCTCTGAAGGACTATTGCACCAGAATGAAGGAAAACTAGAAACA
TATCTATTACATCACAGGTGAGACCAAGGACCAGGTAGCTAAATTTGTGGAATGTCTTTGGAAACATGGCTTAGAAGTGA
TCTATATGATCAAGCCAATTGATGAGTACTGTGTCCAACACTGAAGGAATTTGAGGGGAAGACTTTAGCGTCAGTCACCA
AAGAGGGCTTGGAACTTCCAGAGGATGAAGAAGAAAAAAAGAAACAGGAAGAGAAAAAAACAAAGTTTGAGAACATCTGT
AAAATCATGAAAGACCTATTGGAGAAAAAAGTTGAAAAGGTGGTTGTGTCAAACTGATTGGTGGCGTCTCCATGCTGTAT
TGTCATGAGCATATATGGCTGGACAGCAAACGTGGAAAGAGTCATGAAAGCTCAAGCCCTAAGAGACAACTCAACAATGG
GTTACATGGCAGCAAAGAAACACCTGGAGATAAACCCTGACCATTCCATTACTGAGACCTTAAGGCAAAAGGCAGAGGCA
TATAAGTACAAGTCTGTGTAGGATCTGGTCATCTTGCTTTATGAAACTGCTCTTTTGTCTTCCGGCTTTGGTCTGGAAGA
TCCCCAGACACATGCTAACAGGATCTACAGGATGATCAAACTTGGTGTGGGTATTGATGAAAATGACCCTACTGCTGATG
ATACTACTGAAGAAATGTCACCCCTTGAAGGAGACAATGACACATCATGCATGGAAGAAACAGAC

Alignment

ORF - retro_pabe_1760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.79 %
• Parental protein coverage: 61.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKNNIKLY-VRRVFIMDNCEEL-IPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCLELF
          KKN......V.RVFIMD.CEEL.I..YLNFI..VVDS.DL.LNIS.EMLQQSKILKVIRKNLVKKCLELF
Retrocopy KKNHHQIV<VYRVFIMDSCEEL<ILPYLNFIGKVVDSKDLCLNISHEMLQQSKILKVIRKNLVKKCLELF

Parental  TELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASG-DEMVSLKDYCTRMKENQKHIYY
          T.LAEDKENYKKFY.QFSK.IKL.I..DSQ..KK.SELLRYYTSASG.DEMVSLKDYCTRMKEN.KHIYY
Retrocopy TKLAEDKENYKKFYKQFSKSIKLEIYKDSQHWKKFSELLRYYTSASG>DEMVSLKDYCTRMKEN*KHIYY

Parental  ITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQ-LKEFEGKTLVSVTKEGLELPEDEEEKKKQE
          ITGETKDQVA...FVE.L.KHGLEVIYMI.PIDEYCVQ..LKEFEGKTL.SVTKEGLELPED........
Retrocopy ITGETKDQVAK--FVECLWKHGLEVIYMIKPIDEYCVQH<LKEFEGKTLASVTKEGLELPEDXXXXXXXX

Parental  EKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAKK
          .....FEN.CKIMKD.LEKKVEKVVVSN.LV.SPCCIV.S.YGWTAN.ER.MKAQALRDNSTMGYMAAKK
Retrocopy XXXXXFENICKIMKDLLEKKVEKVVVSN*LVASPCCIVMSIYGWTANVERVMKAQALRDNSTMGYMAAKK

Parental  HLEINPDHSIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGIDEDD
          HLEINPDHSI.ETLRQKAEA.K..KSV.DLVILLYETALLSSGF.LEDPQTHANRIYRMIKLG.GIDE.D
Retrocopy HLEINPDHSITETLRQKAEAYKY-KSV*DLVILLYETALLSSGFGLEDPQTHANRIYRMIKLGVGIDEND

Parental  PTADDTSAAVTEEMPPLEGDDDTSRMEEVD
          PTADDT....TEEM.PLEGD.DTS.MEE.D
Retrocopy PTADDT----TEEMSPLEGDNDTSCMEETD

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	0.06 RPM	1114.11 RPM
SRP007412_cerebellum	0.00 RPM	1481.95 RPM
SRP007412_heart	0.00 RPM	453.18 RPM
SRP007412_kidney	0.00 RPM	612.62 RPM
SRP007412_liver	0.00 RPM	502.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1760 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1760 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501,
Canis familiaris	ENSCAFG00000018036	1 retrocopy	retro_cfam_1094,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Cavia porcellus	ENSCPOG00000002015	1 retrocopy	retro_cpor_1372,
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822, retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760 ,
Pongo abelii	ENSPPYG00000016655	2 retrocopies	retro_pabe_2425, retro_pabe_415,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,