RetrogeneDB ID: retro_nleu_854

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:9141041..9142365(+)
• 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_854
TACATCGATAAAGAAAAACTCAACATAACAAAAGCCATCTGGACCAGAAATCCTGATGATATTATTAATGAGGAGTAAGA
ATTCTACAAAAGCTTGACCAATGACTGGGAAGATCACTTGGCAGTGAAGCATTTTTCAGTTGAAGGACACTTGGAATTCA
GAGCCCTTCTATTTGTCCCACAACATGCTCCTTTTGACTTGTTTGAAAAGAGAAAGAAAAAGAACAACATCAAATTGTAT
GTACACAGAGTTTTCATCATGGATAATTGTGAGGAGCTAATCCCTGTATATCTGAACTTCACTGGAAAGGTGGTGAACTC
AAAGGCTCTCTGTCTAAATATTTCCCTTGAGGTGTTGCCACAAAGCAAAATTTTGAAAGTTATCAGGAAGAATTTGGTTA
AAAAATGCTTAGAACTCTTTACCGAACTGGCAGAAGATAAAGAGAATTACAAGAAGTTCTATGAGTAGCTCTCTAAAAGT
GTAAAGCTTGAAATATATGAAGACTCTCAACATTGGAAGAAGCTTTCAGAGCTGTTAAGATACTACACATTTGCTTCTGG
TGATGAGATGGTTTCCCTCAAGGACTACTGCACCAGAATGAAGGAAAACTAGAAACATATCTATTACATCACAGGTGAGA
CCAAGGACCAGGTAGCTAACTCAGCCTTTGTGGAATGTCTTCGGAAACATGGCTTAGAAGTGATCTATATGATAGAGCCA
ATTGGTGAGTACTGTGTCCAACACTGAAGGAAGTTGAAGGGAAGACTTTAGTATCAGTCACCAAAGAGGGCTTGGAACTT
CCAGAGGATGAAGAAGAAAAAAAGAAACAGGAAGAGAAAAAAAACAAAGTTTGAGAACATCTGCAAAATCATGAAAGACA
TATTGGAGAAAAAAGTTGAAAAGGTGGTTGTGTCAAACTGATTGGCAACGTCTCCATGCTGTATTATCACAAGCATATAT
GGCTGGACAGCAAACATGGAAAGAATCATGAAAGCTCAAGCCCTAAGAGACAACTCAACAACGGGTTACATGGCAGCAAA
GAAACACCTGGAGATAAACCCTGACCATTCCATTATTGAGACCTTAAGGCAAAAGGCAGAGGCAGATAAGTACAAGTCTG
TGCAGGATCTGGTCATCTTGCTTTATGAAACTACTCTTGTCTTCCGGCTTTGGTCTGGAAGATCCCCAGACACATGCTAA
CAGGATCCACAGGATGATTAAACTTGGTGTGGGTATTGATGAAAATAACCCTACTGCTGATACTACTGAAGAAATGTCAC
GCCTTGAAGGAGATGATGACACATCGTGCATGGAAGAAATAGAC

Alignment

ORF - retro_nleu_854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.44 %
• Parental protein coverage: 61.42 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPFDLFE
          YID.E.LN.TK.IWTRNPDDI.NEE..EFYKSLTNDWEDHLAVKHFSVEG.LEFRALLFVP..APFDLFE
Retrocopy YIDKEKLNITKAIWTRNPDDIINEE*-EFYKSLTNDWEDHLAVKHFSVEGHLEFRALLFVPQHAPFDLFE

Parental  NRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCLEL
          .RKKKNNIKLYV.RVFIMDNCEELIP.YLNF...VV.S..L.LNIS.E.L.QSKILKVIRKNLVKKCLEL
Retrocopy KRKKKNNIKLYVHRVFIMDNCEELIPVYLNFTGKVVNSKALCLNISLEVLPQSKILKVIRKNLVKKCLEL

Parental  FTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYY
          FTELAEDKENYKKFYE..SK..KL.I.EDSQ..KKLSELLRYYT.ASGDEMVSLKDYCTRMKEN.KHIYY
Retrocopy FTELAEDKENYKKFYE*LSKSVKLEIYEDSQHWKKLSELLRYYTFASGDEMVSLKDYCTRMKEN*KHIYY

Parental  ITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEEEKKKQEE
          ITGETKDQVANSAFVE.LRKHGLEVIYMIEPI.EYCVQ......G.......K.................
Retrocopy ITGETKDQVANSAFVECLRKHGLEVIYMIEPIGEYCVQH*RKLKGRL*YQSPKRAWNFQRXXXXXXXXXX

Parental  KKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMAAKKH
          ...KFEN.CKIMKDILEKKVEKVVVSN.L.TSPCCI.TS.YGWTANMERIMKAQALRDNST.GYMAAKKH
Retrocopy XXXKFENICKIMKDILEKKVEKVVVSN*LATSPCCIITSIYGWTANMERIMKAQALRDNSTTGYMAAKKH

Parental  LEINPDHSIIETLRQKAEADKNDKSVKDLVILL-YETALLSSGFSLEDPQTHANRIYRMIKLGLGIDEDD
          LEINPDHSIIETLRQKAEADK..KSV.DL...L.....LLSSGF.LEDPQTHANRI.RMIKL..G...D.
Retrocopy LEINPDHSIIETLRQKAEADKY-KSVQDL-VIL>FMKLLLSSGFGLEDPQTHANRIHRMIKL--GVGIDE

Parental  PTADDTSAAVTEEMPPLEGDDDTSRMEEVD
          .......A..TEEM..LEGDDDTS.MEE.D
Retrocopy ---NNPTADTTEEMSRLEGDDDTSCMEEID

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_854 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.

---

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,