RetrogeneDB ID: retro_nleu_2349

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397347.1:129891..131155(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGK
• Ensembl ID: ENSNLEG00000002291
• Aliases: None
• Description: None

Sequence

>retro_nleu_2349
ATGGCGGTGCTCTTTTAAACACTTCAAAATCATTGGAAGAAAGCTACAGCTGGGCTCTGCCTGCTGACCTGGGGAGGCCA
GTGGCTCTATGGAAAACACTGTGATAACCTACTAAGGAGAGCAGCCTGTGAAGAAGCTCAGGTGTTTGGCAATCAACTCA
TTCCTCCCAATGCACAAGTGAAGAAAGAATCTGTTTTTCTCAATCCTGCAGCTTGCAAAGGCAAAGCCAGGATTCTATTT
GAAAAAAATGCTGCCCCGATTTTACATTTATCCTGGCATAGGTGTGACTATTGTTAAGACAGATTATGAGGGACAAGCCA
AGAAATTACTGGAACTGATAGAAAACACATAGGTGATCATTGTTGCAGGAGGAGATGGGACACTGCAGGAGGTTGTTACT
GGAGTTCTTCGATGAACAGATGAGGCTACCTTCAGTAAGATTCCCATTAGATTTATCCCACTGGGAGAGACCAGTAGTTT
GAGTCATAACCTCTTTACTGAAAGTGGAAACAAAGTCCAACATATTACTGATGCTACACTTGCCATTGTGAATGGAGAGA
CAGTTCCATTTGATGTCTTGCAGATCAAGGGTGAAAAGGAACAGCCTGTGTTTGCAATGACCGGCCTTTGATGGGGATCC
TTCAGAGATGCTGGCATCAAAGTTAGCAGGTACTGATATCTTGGGCCTCTAAAAATCAAAGCAGCCCACTTTTTCAGCAC
TCTTAAGGAGTGGCCTCAGACTCATGAAACCTCTATCTCGTATACGGGACCTACAGAGAGACCTGCCAATGAACCAGAGG
AGACCCCTGTACAAAGGCCTTCTTTGTACAGGAGAATATTACAGAGGCTTGCATCTTACTGGGCACAACCACAGGATGCC
CTTTCCCAAGAGGTGAGCCGAGAGGTCTGGAAAGATGTGCAGTTGTCCACCATTGAACTGTCCATCATAACACGGAACAA
TCAGCTTGACCGAACACGCAAAGATTTTATGAACATCTGCATTGAAGCCAACACCGTCAGCAAAGGAGACTTTGTAACTA
TAAGAAGTCGAAAGGTGAGAAAAGCCAAGCTGGACACCGAGGGCATGGAGTGTCTCCAAGCCAGCCAGTACACTTCGCTT
GTCCCCAAGGAAGCAGGGAGCTCTTTTAGCATTGACAGTGAGGAGTATGAAGTGATGCCTGTGGAGGTGAAACTGCTCCC
CAGGAAGCTGCAGTTCTTCTGTGATCCTAGGAAGAGAGAACAGATGCTGGCAAGCCCCACCCAG

Alignment

ORF - retro_nleu_2349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTVFFKTLRNHWKKTTAGLCLLTWGGHWLYGKHCDNLLRRAACQEAQVFGNQLIPPNAQVKKATVFLNPA
          M.V.F.TL.NHWKK.TAGLCLLTWGG.WLYGKHCDNLLRRAAC.EAQVFGNQLIPPNAQVKK..VFLNPA
Retrocopy MAVLF*TLQNHWKKATAGLCLLTWGGQWLYGKHCDNLLRRAACEEAQVFGNQLIPPNAQVKKESVFLNPA

Parental  ACKGKARTLFEKNAAPILHLS-GMDVTIVKTDYEGQAKKLLELMENTDVIIVAGGDGTLQEVVTGVLRRT
          ACKGKAR.LFEKNAAPILHLS.G..VTIVKTDYEGQAKKLLEL.ENT.VIIVAGGDGTLQEVVTGVLR.T
Retrocopy ACKGKARILFEKNAAPILHLS>GIGVTIVKTDYEGQAKKLLELIENT*VIIVAGGDGTLQEVVTGVLR*T

Parental  DEATFSKIPIGFIPLGETSSLSHTLFAESGNKVQHITNATLAIVKGETVPLDVLQIKGEKEQPVFAMTGL
          DEATFSKIPI.FIPLGETSSLSH.LF.ESGNKVQHIT.ATLAIV.GETVP.DVLQIKGEKEQPVFAMTGL
Retrocopy DEATFSKIPIRFIPLGETSSLSHNLFTESGNKVQHITDATLAIVNGETVPFDVLQIKGEKEQPVFAMTGL

Parental  RWGSFRDAGVKVSKYWYLGPLKIKAAHFFSTLKEWPQTHQASISYTGPTERPPSEPEETPVQRPSLYRRI
          .WGSFRDAG.KVS.Y.YLGPLKIKAAHFFSTLKEWPQTH..SISYTGPTERP..EPEETPVQRPSLYRRI
Retrocopy *WGSFRDAGIKVSRY*YLGPLKIKAAHFFSTLKEWPQTHETSISYTGPTERPANEPEETPVQRPSLYRRI

Parental  LRRLASYWAQPQDALSQEVSPEVWKDVQLSTIELSITTRNNQLDPTSKEDFLNICIEPDTISKGDFITIG
          L.RLASYWAQPQDALSQEVS.EVWKDVQLSTIELSI.TRNNQLD.T.K.DF.NICIE..T.SKGDF.TI.
Retrocopy LQRLASYWAQPQDALSQEVSREVWKDVQLSTIELSIITRNNQLDRTRK-DFMNICIEANTVSKGDFVTIR

Parental  SRKVRNPKLHAEGTECLQASQCTLLIPEGAGGSFSIDSEEYEAMPVEVKLLPRKLQFFCDPRKREQMLTS
          SRKVR..KL..EG.ECLQASQ.T.L.P..AG.SFSIDSEEYE.MPVEVKLLPRKLQFFCDPRKREQML.S
Retrocopy SRKVRKAKLDTEGMECLQASQYTSLVPKEAGSSFSIDSEEYEVMPVEVKLLPRKLQFFCDPRKREQMLAS

Parental  PTQ
          PTQ
Retrocopy PTQ

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_2349 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013589	1 retrocopy	retro_cjac_3228,
Gorilla gorilla	ENSGGOG00000008821	1 retrocopy	retro_ggor_3061,
Loxodonta africana	ENSLAFG00000002479	1 retrocopy	retro_lafr_403,
Microcebus murinus	ENSMICG00000002561	1 retrocopy	retro_mmur_850,
Macaca mulatta	ENSMMUG00000021017	1 retrocopy	retro_mmul_2637,
Mus musculus	ENSMUSG00000029916	1 retrocopy	retro_mmus_1130,
Nomascus leucogenys	ENSNLEG00000002291	1 retrocopy	retro_nleu_2349 ,
Pongo abelii	ENSPPYG00000018064	1 retrocopy	retro_pabe_3812,
Pan troglodytes	ENSPTRG00000019775	2 retrocopies	retro_ptro_3269, retro_ptro_3311,