RetrogeneDB ID: retro_nleu_1501

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397296.1:4070486..4071204(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: T
• Ensembl ID: ENSNLEG00000011552
• Aliases: None
• Description: None

Sequence

>retro_nleu_1501
GAGTGTGCATCGAAGAGCCTGCAGTACCGAGTGGACTACCTGCTGAGAGCCACGAAGCGTGAGCAACAGGCCAGGCATTG
AGAAGGGTGACCATGTAGAGTGAAAGTGGCACATAGGCCTGGAGGAGAGCAAGTTGTGGCTATGCTTCAAGGAGCTCACC
AATGACATGATCACCACCAAGAATGCCAGGAAGTTGTTTCCAGTGCCGAGCATGTCTGGCTTGGCTTTAAGAGCCATGTA
CTCCTTCTTGCTGGACTTCGTGGAGGCCGACAGTAAGCGCTGGAAGAAAACCAGAAGTGGGAACCAGGAATGGGTGCCAG
AGGGCAAACCTGAGCTGTAGGCCCTCAGGTGTGTGCCCATCCAGCCCAATTCCCCCAACTTAGGGCGCTACTGGATGAAG
ATGCCCATCTCCCTCAGCAAAGTCAAGATCAACAACTAGCTACACAGAGGGGGCCTGATCATGTCAAACTCCTTAATAAG
CACCAGCCTCGAATTCACATAGTGAGAGTGGGGTGTCCACAACACATAATCACTAGCCATTGCTTTCCGAGACCTAGTTC
ATAAATAACTGTGACAGCTTATCAGAATGAAGAGCTCAAAGCTGAAATTTAAACACAATCCATTTGCAAAAGCTTCCCTG
GATGCAAAGGAAAGAAGCAATTACAAAGATATGATGGAAGAACTCCAAGGCAGCCAGGAAGAACCCCAATCTAGGTAC

Alignment

ORF - retro_nleu_1501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.59 %
• Parental protein coverage: 54.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ESAGKSLQYRVDHLLSAVESELQA-GSEKGDPTERELRVGLEESELWLRFKELTNEMIVTKNGRRMFPVL
          E.A.KSLQYRVD.LL.A...E.QA.G.EKGD..E.....GLEES.LWL.FKELTN.MI.TKN.R..FPV.
Retrocopy ECASKSLQYRVDYLLRATKREQQA>GIEKGDHVE*KWHIGLEESKLWLCFKELTNDMITTKNARKLFPV-

Parental  KVNVSGLDPNAMYSFLLDFVAADNHRWKYV---NGEWVPGGKPEPQAPSCVYIHPDSPNFGAHWMKAPVS
          ....SGL...AMYSFLLDFV.AD..RWK.....N.EWVP.GKPE..A..CV.I.P.SPN.G..WMK.P.S
Retrocopy -PSMSGLALRAMYSFLLDFVEADSKRWKKTRSGNQEWVPEGKPEL*ALRCVPIQPNSPNLGRYWMKMPIS

Parental  FSKVKLTNKLNGGGQIMLNS-LHKYEPRIHIVRVGGPQRMITSHCFPE-TQFIAVTAYQNEEITALKIKY
          .SKVK..N.L..GG.IM.NS.L.K..PRIHIVRVG.PQ..ITSHCFP.....I.VTAYQNEE..A..I..
Retrocopy LSKVKINN*LHRGGLIMSNS<LNKHQPRIHIVRVGCPQHIITSHCFPRPSS*ITVTAYQNEELKA-EI*T

Parental  NPFAKAF-LDAKERSDHKEMMEEPGDSQQPGYSQW
          ....K.F.LDAKERS..K.MMEE...SQ....S..
Retrocopy QSICKSF>LDAKERSNYKDMMEELQGSQEEPQSRY

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_1501 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006236	1 retrocopy	retro_chof_209,
Equus caballus	ENSECAG00000007994	1 retrocopy	retro_ecab_568,
Microcebus murinus	ENSMICG00000016122	1 retrocopy	retro_mmur_1130,
Nomascus leucogenys	ENSNLEG00000011552	1 retrocopy	retro_nleu_1501 ,