RetrogeneDB ID: retro_nleu_1904

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397315.1:674185..675233(+)
• Located in intron of: ENSNLEG00000001677

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000026903
• Aliases: None
• Description: None

Sequence

>retro_nleu_1904
ATGGGGACACAGAAGGTCACCCCAGCTCTGATCATTGCCATCACAGTTGCTACAATCGGCTCTTTCCAATTTGGCTACAA
CACTGGACTCATCAATGCTCCTGAGATGATCATAAAGGAATTTATCAATAACATTTTGAGTGACCAGGCAAATATCCCTC
CCTCTGAGATGTTGCTCATGTCCCTCTGGTCCTTGTCTGTGGCCATATTCTCCATTGTTGGTATGACTGGCTCCTTTTCT
GTTAGACTCTTTGTCAACTACTTTGACAGGTGCAATTCAATGCTTATCGTCAACCTGTTGGCTGTCTCTGGTGGCTGCCT
TACGGGATTGTGTAAAGTGGCCGAGTTGGTTGAAATGCTGATCCTGGGCTGCTTGGTTATTGGCCTCTTCTGTGGACTGC
GCACAGGTTTTGTGCCCATGTACATTGGAGAGATCTCACCTACTGCCCTGCAGGGTACCTTTGGCACTCTCAACCAGCTG
GGCATCGTCGGAATTCTGGTGGCCCAGATCTTTGATCTGGAATTCAAATTCATCCTTGGGTGTGAAGAGCTATGGCCGGT
GCTATTGGGCTTTACCATCCTTCCAGCTATCCTACAAAGTGCAGCCCTTCCATTTTGCCCTGAAAGTCCCAGGTTTTTGC
TCATTAACAGAAGAGGAGAATGCTAAGTAGATCCTCCAGCGGTTGTGGGGCACCCAGGATGTATCCCAAGACAACCAGGA
GATGCAAGATGAAAGTGCAAGGATGTCACAAGAAAAGCAAGTCACCGTGCTGGAGCTCTTTAGAGTATCCAGCTACTGAC
AGCCAATCATCATTTCCATCGTGCTCCAGCTCTCTCGACAGCTCTCTGGAATCAATGCTGTGTTCTATTACTCAACAGGA
ATCTTCAAGGATGCAGGTGTTCAAGAGCCCATCTATGACACCATTGGTGCAGGTGTGTTTAATACTGTCTTCACTGTTTC
CCTATTTCTGCTGGAAAGGGCAGGAAGAAGGACTCTGCATATGATAGGCCTTGGAGGGATGGCTTTTTCTTCCATGCTCA
TGACTGTT

Alignment

ORF - retro_nleu_1904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.2 %
• Parental protein coverage: 70.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGTQKVTPALIFAITIATIGCFQFGYNIGVINAPEKIIKEFINKTLTDKGNAPPSEVLLTSLWSLSVAIF
          MGTQKVTPALI.AIT.ATIG.FQFGYN.G.INAPE.IIKEFIN..L.D..N.PPSE.LL.SLWSLSVAIF
Retrocopy MGTQKVTPALIIAITVATIGSFQFGYNTGLINAPEMIIKEFINNILSDQANIPPSEMLLMSLWSLSVAIF

Parental  SVGGMIGSFSVGLFVNRFGRRNSMLIVNLLAVTGGCFMGLCKVAKSVEMLILGRLVIGLFCGLCTGFVPL
          S..GM.GSFSV.LFVN.F.R.NSMLIVNLLAV.GGC..GLCKVA..VEMLILG.LVIGLFCGL.TGFVP.
Retrocopy SIVGMTGSFSVRLFVNYFDRCNSMLIVNLLAVSGGCLTGLCKVAELVEMLILGCLVIGLFCGLRTGFVPM

Parental  YIGELSPTALQGAFGTLNQLGIVVGILVAQIFGL--KFILGSEELWPLLLGFTIIPTILQSVALPFCPES
          YIGE.SPTALQG.FGTLNQLGIV.GILVAQIF.L..KFILG.EELWP.LLGFTI.P.ILQS.ALPFCPES
Retrocopy YIGEISPTALQGTFGTLNQLGIV-GILVAQIFDLEFKFILGCEELWPVLLGFTILPAILQSAALPFCPES

Parental  -PRFLLINRKEEENAKRILQRLWGTQDVSQDIQEMKDESARMSQEKQVTLLELFRVSSYRQPLIISIVLQ
          .P.F......EEENAK.ILQRLWGTQDVSQD.QEM.DESARMSQEKQVT.LELFRVSSY.QP.IISIVLQ
Retrocopy >PGFCSLT--EEENAK*ILQRLWGTQDVSQDNQEMQDESARMSQEKQVTVLELFRVSSY*QPIIISIVLQ

Parental  LSQQLSGINAVFYYSRGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCST
          LS.QLSGINAVFYYS.GIFKDAGVQEPIY.TIGAGV.NT.FT.VSLFL.ERAGRRTLHMIGLGGMAF.S.
Retrocopy LSRQLSGINAVFYYSTGIFKDAGVQEPIYDTIGAGVFNTVFT-VSLFLLERAGRRTLHMIGLGGMAFSSM

Parental  LMTV
          LMTV
Retrocopy LMTV

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_1904 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904 ,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,