RetrogeneDB ID: retro_nleu_714

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397270.1:44792876..44794225(-)
• 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_714
GAGGAGGAGGTGGAGACTTTTGCCTTTCAGACAGAAATTGCCCAACTCAGGTCTCTTATTATCAATATCTTCTATTCCAA
CAAGCAGATTTTTCCTTCAAGAGTTGATTTCTAATGCTTCTAATGCCTTGGACAAGATTCTCTGTGAGAGCCTGGCAGAC
ACTTACAAGTTGGACAGTGACAAAGAGCTGAAAATTGACATCATGCCCAACCCTCAGGAATGCACTCTGACTTTGGTGGA
CACAGGCACTGGCATGACAAAGCTGATTTCATAAATAATTTGGGAACCATTGCCAAGTCTGATACTGAAGAATTTATGGA
GGCTCTTCAGGCTGGTGCAGACATCTCCATGACTGTCAATTTGGTGTTGGCTTTCATTCTGCCTATCTGGTGGCAGAGAA
AGTGGTTGTGATCACAAAGCACAATGATGATGAACAGTGAGCCTGGGAGTTTTCTGGTGGGGGTTCCTTCACTGTATGTG
CTGACCATGGCAGGGGTACCAAAATGATCCTCCACCTTAAAGAAAACCAGACAGAGTACTGAGAAGAGAGATAAGTCAAA
GATGCAGTGAAAAAGCACTCACAGTTCATAGGCTAACCCATCACCCTCTATCTGAGGAAAGAAAGAGAGAAGGAAATCAG
TGATGATGAGACAGAGGAAGAGAAAGGCAAGAAATAATAGGAAGATAAAGATAATGAGGAAAGACTCAAGATTGAAAATG
TGGGTTCAAATGAGGATGACACTGGTAAGGATAATTAAAAGAAAACCGAGAAGATCAAAGAGAAATACATTGATCAGGAA
GAACTAAACAAGACCAAGCCTATTTGGACAAGAAACCATGATTACATCACCCAGGAGGAGTATGGAGAATTCTGTAACAG
CCACACTAATGACTGGGAAGACCACTTGGCAGTCAAACACTTCTCTATAGAAGGTCAGTTGGAATTCAGGGCATTGTTGT
TCATCCCTTAACGGGCTCCTTTTGACCTCTTTGAGAACAATAAGAATAAAGACACCATCAAACTCTACGTCCTTCATGTG
TTCATCGTGCACAGCTGTGATGAGTTGATACCAGAGGATCTCAACTTTATCTGTGGTATGGTTGACTCTGAGGATCTATC
CCTGAACATTTGAGAAATGCTCCAGGAGAGCAAAATCTTGAAAGTCATTCACAGAAACATTGTTAAGTGGTGCCTTGAAC
TCTTCTCTGAGTTGGCAGAAGACAAAGAGAATTACAAGAAATTCTATGAGGCATCCTCTAAAAATCTAATGTTTGGAATC
CCCAAGGACTCCCCTAACTGGCGACACCTGTCTGAGCTGCTGCACTTTCACAGCTCCCAGTCTGGAGAT

Alignment

ORF - retro_nleu_714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.37 %
• Parental protein coverage: 62.65 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEEVETFAFQAEIAQLMSLIINTFYSNKEIF-LRELISNSSDALDKIRYESLTDPSKLDSGKELHINLIP
          EEEVETFAFQ.EIAQL.SLIIN.FYSNK.IF.L.ELISN.S.ALDKI..ESL.D..KLDS.KEL.I...P
Retrocopy EEEVETFAFQTEIAQLRSLIINIFYSNKQIF>LQELISNASNALDKILCESLADTYKLDSDKELKIDIMP

Parental  NKQDRTLTIVDTGIGMT-KADLINNLGTIAKSGTKAFMEALQAGADISMI-GQFGVGFYSAYLVAEKVTV
          N.Q..TLT.VDTG.GMT.KAD.INNLGTIAKS.T..FMEALQAGADISM...QFGVGF.SAYLVAEKV.V
Retrocopy NPQECTLTLVDTGTGMT<KADFINNLGTIAKSDTEEFMEALQAGADISMT<CQFGVGFHSAYLVAEKVVV

Parental  ITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITL
          ITKHNDDEQ.AWE.S.GGSFTV..D.G....RGTK.ILHLKE.QTEY.EER..K..VKKHSQFIG.PITL
Retrocopy ITKHNDDEQ*AWEFSGGGSFTVCADHG----RGTKMILHLKENQTEY*EER*VKDAVKKHSQFIG*PITL

Parental  FVEKERDKEVSDDEAEEKEDKEEEKEEKESEDKPEIEDVGSDEEEEEKKDGDKKKKKKIKEKYIDQEELN
          ...KER.KE.SDDE.EE...K......K..E....IE.VGS.E....K.....KK..KIKEKYIDQEELN
Retrocopy YLRKEREKEISDDETEEEKGKK**E-DKDNEERLKIENVGSNEDDTGK--DN*KKTEKIKEKYIDQEELN

Parental  KTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPFDLFENRKKKNNI
          KTKPIWTRN.D.IT.EEYGEF..S.TNDWEDHLAVKHFS.EGQLEFRALLF.P.RAPFDLFEN.K.K..I
Retrocopy KTKPIWTRNHDYITQEEYGEFCNSHTNDWEDHLAVKHFSIEGQLEFRALLFIP*RAPFDLFENNKNKDTI

Parental  KLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCLELFTELAEDK
          KLYV..VFI...C.ELIPE.LNFI.G.VDSEDL.LNI..EMLQ.SKILKVI..N.VK.CLELF.ELAEDK
Retrocopy KLYVLHVFIVHSCDELIPEDLNFICGMVDSEDLSLNI-*EMLQESKILKVIHRNIVKWCLELFSELAEDK

Parental  ENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGD
          ENYKKFYE..SKN...GI..DS.N...LSELL....S.SGD
Retrocopy ENYKKFYEASSKNLMFGIPKDSPNWRHLSELLHFHSSQSGD

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_714 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,