RetrogeneDB ID: retro_nleu_822

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397274.1:5490295..5492409(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90AA1
• Ensembl ID: ENSNLEG00000015925
• Aliases: None
• Description: None

Sequence

>retro_nleu_822
GAGGAGGAGGTGGAGACTTTTGCCTTTCAGGCAGAAATTGCCCAACTCATGTTTCTCATCATCAATACCTTCTAATCTAA
CAAGGAGATTTTCCTTTGGGATTTGATCTCTAATGCTTCTGATGCCTTGGACAAGATTCGCTATGAAAGCCTAACAGATC
CTTCCAAGTTGGACAGTGGTAAAGTGCTGAAAATTGACATCATCCCCAATACTCAGGAACATACCCTGACTTTGGTGGAC
ATAGGCATTGGCATGACCAAAGCTGATCTAATAAATAATTTGGGAATCATTGCCAAGTCTCGTACTAAAGCATTCATGGA
GGCTCTTTGGGCTGGTACAGACATCTCCATGATTGGGCAATTTGGTGTTGGCTTTTATTCTGCCTACCTGGTAGCAGAGA
AAGTGGTTGTGATCACAAAGCCCAATGATGATGGTATGTCTGGGAGTCTTCTACTGGAGGTTCCTTCACTGTGTGTGCCG
ACCATGGTGAGCATATTGGCAGGGGTACCAAAGTGATCCTCCACCTTAAAGAAGATCAGACAGAATACTTAGAAGAGAGG
CGGGTCAAAGCAGTAGTGAAGAAGCACTTTCAGTTCCTAGGCTATCCCATCACCCTTTATCTGGAGAAGGAACGAGAGAA
AGAAATTAGTGATGATAAGGCAGAGGAAGAGAAAGGTGAGAAAGAAGAGGAAAATAAAGACGATGAAGAAAAGCCCAAGA
TCAAAGATGTGGGTTCAGATGAGGAGGATGACAGTGGTAAGGATAAGAAGAAGAAAACTAAGAAGATCAAAAAGAAATAC
ATTGATCAGAAAGAACTAAACAAGACCAAGCCTATTTGGACCAGAAACACTGAAGACACCACCCAAGAGGAGTATGGAGA
ATTCTATAAGAGCCTCACCAATGACTGGAAAGACCACTTGGCAGTCAGGTACTTTTCTGTAGAAGGTCAATTGGAATTCA
GGGCATTGCCACTCCTTCCTCATCAGGCTCCCTTTGATCTTTTTGAGAACAAGAAGAAAAAGAACAACATCAAACTCTAT
GTCCATCGTGTGTTCATCAGGGACAGCTGTGATGACTTGATACCAGAGTGTCTCAACTTTATCCGTGGTGTGGTTGACTC
TGAGGATTTGCCCCTGAACATCTCCCGAGAAATGCTCCAGCAGAGCAAAATCTTGAGTCATTCACAAAAACATTGTTAAG
AAGTGCCTTGAGCTCTTCGCTGAGCTGGTGGAAGACAAGGAGAATTACAAGAAATTCTATGAGGCATTCTCTAAAAATCT
CAAGCTTGGCATCCACGAGGACTCCACTAACTGATGCCACCCATCTGAGCTGCTGTATTATCACACCTCCCAGTCTGGAG
ATGAGATGACATCTTTGTTAGAGTATGTTTCTTGCATGAAGGAGATACAGAAGTCCATCTATTACATCACTGGTGAGAGC
AAAGAGCAGGTTGCCAACTCAGCTTTTGTGAAGCGAGTATGGAAACGGAGCTTCAGGGTGGTGTATATGACCGAACCCAT
TGACGGCTATGTGTGCAGCAACTAAAGGAGTTTGATGGCAAGAGCCTGGTCTCAGTTACCAAGGAGGGCCTGGATCTACT
TGAGGATGGGGAGGAGAAGAAAATGGAAGACAGGAAGGCAAAGTTTGAGAACCGCTGCAAGATCATGAAAGAAATCTTAG
ATAAGAAGGTTGAGACGGTGACAATCTCCAATAGGCTTGTGTCTTCATCCTGCTGCATTGTGACCAGCACCTACAGCTGG
ACAGCCAATATGGAGCAGATCATGAAAGCCCAGGCACTTCGGGTCAACTCCACCGTGGACTATATGATGGCCAAAAAGCA
CCTGGAGATCAACCCCAACCACCCCATTGTGGAGATGCTGTGGCAGAAGGCTGAGGCAGACAAGAACGACAAGGCAGTCA
AGGACCTGGTGGTGCTGCCATTAGAAACTGCCTTGCTGTCTTCTGGCTTTTCCCTTGAGGATCCCCAGACCCATTCCAAC
CGCATCTACCACATGATCAAGCTAGGTCTAGGTATTGATGAAGATTAAGTGGCAGCAGAGGAACACAGTGCTGTGGTTCC
TGATGAGATCACCCCTCTTGAGGGTGATGGGGAT

Alignment

ORF - retro_nleu_822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.49 %
• Parental protein coverage: 97.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGKELHINLIPN
          EEEVETFAFQAEIAQLM.LIINTF.SNKEIFL..LISN.SDALDKIRYESLTDPSKLDSGK.L.I..IPN
Retrocopy EEEVETFAFQAEIAQLMFLIINTF*SNKEIFLWDLISNASDALDKIRYESLTDPSKLDSGKVLKIDIIPN

Parental  KQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITK
          .Q..TLT.VD.GIGMTKADLINNLG.IAKS.TKAFMEAL.AG.DISMIGQFGVGFYSAYLVAEKV.V...
Retrocopy TQEHTLTLVDIGIGMTKADLINNLGIIAKSRTKAFMEALWAGTDISMIGQFGVGFYSAYLVAEKV-VVIT

Parental  HNDDEQ-YAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFV
          ...D...Y.WESS.GGSFTV..D.GE..GRGTKVILHLKEDQTEYLEERR.K..VKKH.QF.GYPITL..
Retrocopy KPNDDG<YVWESSTGGSFTVCADHGEHIGRGTKVILHLKEDQTEYLEERRVKAVVKKHFQFLGYPITLYL

Parental  EKERDKEVSDDEAEEKEDKEEEKEEKESEDKPEIEDVGSDEEEEEKKDGDKKKKKKIKEKYIDQEELNKT
          EKER.KE.SDD.AEE.E..E.E.E.K..E.KP.I.DVGSDEE....KD..KKK.KKIK.KYIDQ.ELNKT
Retrocopy EKEREKEISDDKAEE-EKGEKEEENKDDEEKPKIKDVGSDEEDDSGKD-KKKKTKKIKKKYIDQKELNKT

Parental  KPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPFDLFENRKKKNNIKL
          KPIWTRN..D.T.EEYGEFYKSLTNDW.DHLAV..FSVEGQLEFRAL...P..APFDLFEN.KKKNNIKL
Retrocopy KPIWTRNTEDTTQEEYGEFYKSLTNDWKDHLAVRYFSVEGQLEFRALPLLPHQAPFDLFENKKKKNNIKL

Parental  YVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKIL-KVIRKNLVKKCL-ELFTELAEDK
          YV.RVFI.D.C..LIPE.LNFIRGVVDSEDLPLNISREMLQQSKIL.....K.L....L.ELF.EL.EDK
Retrocopy YVHRVFIRDSCDDLIPECLNFIRGVVDSEDLPLNISREMLQQSKIL<ESFTKTLLRSAL<ELFAELVEDK

Parental  ENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYYITGETKDQ
          ENYKKFYE.FSKN.KLGIHEDS.N....SELL.Y.TS.SGDEM.SL..Y...MKE.QK.IYYITGE.K.Q
Retrocopy ENYKKFYEAFSKNLKLGIHEDSTN*CHPSELLYYHTSQSGDEMTSLLEYVSCMKEIQKSIYYITGESKEQ

Parental  VANSAFVERLRKHGLEVIYMIEPIDEY-CVQQLKEFEGKTLVSVTKEGLELPEDEEEKKKQEEKKTKFEN
          VANSAFV.R..K....V.YM.EPID.Y.CVQQLKEF.GK.LVSVTKEGL.L.ED.EE.KK.E..K.KFEN
Retrocopy VANSAFVKRVWKRSFRVVYMTEPIDGY<CVQQLKEFDGKSLVSVTKEGLDLLEDGEE-KKMEDRKAKFEN

Parental  LCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAKKHLEINPDH
          .CKIMK.IL.KKVE.V..SNRLV.S.CCIVTSTY.WTANME.IMKAQALR.NST..YM.AKKHLEINP.H
Retrocopy RCKIMKEILDKKVETVTISNRLVSSSCCIVTSTYSWTANMEQIMKAQALRVNSTVDYMMAKKHLEINPNH

Parental  SIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGIDEDDPTADDTSA
          .I.E.L.QKAEADKNDK.VKDLV.L..ETALLSSGFSLEDPQTH.NRIY.MIKLGLGIDED...A...SA
Retrocopy PIVEMLWQKAEADKNDKAVKDLVVLPLETALLSSGFSLEDPQTHSNRIYHMIKLGLGIDED*VAAEEHSA

Parental  AVTEEMPPLEGDDD
          .V..E..PLEGD.D
Retrocopy VVPDEITPLEGDGD

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_822 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 11 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501,
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,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Nomascus leucogenys	ENSNLEG00000006510	1 retrocopy	retro_nleu_993,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822 , retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,