RetrogeneDB ID: retro_nleu_2757

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397420.1:219398..220754(-)
• Located in intron of: ENSNLEG00000010407

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1A
• Ensembl ID: ENSNLEG00000017836
• Aliases: None
• Description: None

Sequence

>retro_nleu_2757
ATGCGTGAGTGCATCTCCATCACATTGGCCAGGCTGGTGTCCAGGTTGGCAATGCCTGCTGGGAGCCCTACTGCCTGGAA
CATGGCATCCAGCCCAACAGCCAGATGCCAAGTGACAAGACCACTTGGGGAGGAGATGACTCCTTCAACAGCTTCTTCAG
TGAGATGGGCTCCGGCAAGCATGTGCCTAGGGCAGTGTTTCTAGACCTGAAACTCATGGTAATTGATGATGAAGTTTGCA
TTGGCACCTACCACCAGCTCTCCCACCCTGAGCAGCTCATCACAGGCAAGGAAGACGCTGTCAGTAACTATGCCTGAAGG
CACTACACCATTGGCCAGGAGATCACTGACTTCGTTTTGGACCAGATTTGTAAACTGGCTGACCAGTGCATGGATCTCCG
AGGCTTCTTGGTTTTCCATAGCTTTGGTGAAGGAATTGGTTCTGGGTTCACCTCCCTGCTCATGGAACAACTCCCGGTTG
ATTACGGCAAGAAGTCCAAGCTGGAGTTCTCCATTTACTCCACCACCCCAGGTTTCCACAGCTGTAGTTGAGCCCTACAA
CTCCATCCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGTCTTCATGGTAGACAATGAGGCCACCTATGATATCT
GGCACAGAACCTTGATACTGAACGCCCAACCTATACTAAACTGAATAGGTTGATAGGTCAAATTTTGTCCTCCATCACTG
CTTCCCTGAGATTTGATGGAGCCCTGAATGTTGATCTGACAGAATTCCAGACCAAGCTGGTACCCTATCCCCCCATCCAC
TTCCCTCTGGACACATATGCCCCGTTATCTCTGCTGAGAAAGCCTACCATGAAACAGCTTTCTGTAGCAGAGACTGCCAG
TGCTTGCTTTGAGCCTGCCAACCAGATGATGAAATGTGAGCCTTGCCATGGTAAATACATGGTTTGCTGCCTGTTTTACC
ATGGCGACATGGTTCTCAAAGATGTCAATGCTGCCATTGCCACCATCAAGACCAAGCATATCATCCAATCTGTGGTTTGG
TGCCCCCATGGCTTCCAGGTTGGCATTAACTGCCAGCCCTCCCACTGTGGTGACTGGTGGAGACCTGGTCAAGATACAGA
GAGCTGTATGCATGCTGAGCAATACCACAGCCATTGCTGAGGCCTGGGCTTGCCTGGGCCACAAGTTTGACTTGAATGTA
TGTCAAGATGCTTTTGTTCACTGGTGCATGGGTGAGAGAAGGGAGGAAGGAGAGTTTTCTGAGGCTGGTGAGGACATGAC
TGCCCTTGAGAAGGATTATAAGGAGGTTGGTGTAGATTCTGTTGAAGGAGAAGGTGAGGAAGAAAGAGAGGAATAC

Alignment

ORF - retro_nleu_2757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MRECISI-HVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVD
          MRECISI.H.GQAGVQ.GNACWE.YCLEHGIQP..QMPSDKT..GGDDSFN.FFSE.G.GKHVPRAVF.D
Retrocopy MRECISI<HIGQAGVQVGNACWEPYCLEHGIQPNSQMPSDKTTWGGDDSFNSFFSEMGSGKHVPRAVFLD

Parental  LEPTVID-EVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVF
          L...VID.EV..GTY.QL.HPEQLITGKEDA..NYA..HYTIG.EI.D.VLD.I.KLADQC..L.GFLVF
Retrocopy LKLMVIDDEVCIGTYHQLSHPEQLITGKEDAVSNYA*RHYTIGQEITDFVLDQICKLADQCMDLRGFLVF

Parental  HSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIY-PAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNE
          HSFG.G.GSGFTSLLME.L.VDYGKKSKLEFSIY.P.PQVSTAVVEPYNSILTTHTTLEHSDC.FMVDNE
Retrocopy HSFGEGIGSGFTSLLMEQLPVDYGKKSKLEFSIY>PPPQVSTAVVEPYNSILTTHTTLEHSDCVFMVDNE

Parental  AIYDICRR-NLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYA-PV
          A.YDI..R.NLD.ERPTYT.LNRLIGQI.SSITASLRFDGALNVDLTEFQT.LVPYP.IHFPL.TYA.PV
Retrocopy ATYDIWHR<NLDTERPTYTKLNRLIGQILSSITASLRFDGALNVDLTEFQTKLVPYPPIHFPLDTYA<PV

Parental  ISAEKAYHE-QLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFV
          ISAEKAYHE.QLSVAE...ACFEPANQM.KC.P.HGKYM.CCL.Y.GD.V.KDVNAAIATIKTK..IQ.V
Retrocopy ISAEKAYHE>QLSVAETASACFEPANQMMKCEPCHGKYMVCCLFYHGDMVLKDVNAAIATIKTKHIIQSV

Parental  DWCPTGFKVGINYQ-PPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGM
          .WCP.GF.VGIN.Q.PPTVV.GGDL.K.QRAVCMLSNTTAIAEAWA.L.HKFDL.....AFVHW..GE..
Retrocopy VWCPHGFQVGINCQ>PPTVVTGGDLVKIQRAVCMLSNTTAIAEAWACLGHKFDLNVCQDAFVHWCMGERR

Parental  EEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          EEGEFSEA.EDM.ALEKDY.EVGVDSVEGEGEEE.EEY
Retrocopy EEGEFSEAGEDMTALEKDYKEVGVDSVEGEGEEEREEY

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_2757 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus	ENSDNOG00000004121	1 retrocopy	retro_dnov_43,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223,
Homo sapiens	ENSG00000167552	1 retrocopy	retro_hsap_3313,
Nomascus leucogenys	ENSNLEG00000017836	2 retrocopies	retro_nleu_245, retro_nleu_2757 ,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72,