RetrogeneDB ID: retro_nleu_369

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:52792945..52793529(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6
• Ensembl ID: ENSNLEG00000026948
• Aliases: None
• Description: None

Sequence

>retro_nleu_369
GAGGAACCAACAGAGCCCTCCATCTCCAAAGCTGCTGCCAAACCAGCAGCAACATGGGCCCCTCTAGCCATGACCAAAGC
TGAGCCAGTTATCCCATCCCCCAGGCACCTGAGAAAACCAAGGAGCCCCCCCAGTTGATCTCTCCAAAGTGGTGATCAAG
TTTAACAAAGACCAGCTGGAGGAGTTCAAGGTGGCCTTCAAGCTGTTTAACTGAGTGGGGGATGGCAAGATCCTGTACAG
CCAGTATGGGGACATGATGGGGGTCCTGGACCAGAACCTCACCAGTGCCAAGGTGATGAAGGTCCTGGGGAACCCCAAGA
GTGATGAGCTGAAGTCTCGGCATGTGGACTTCAAGACTTTCCTGCCCATGCTCCAGGCAGCAGCCAAGAAGCGAAACCAA
GGCACATATGAGGATTACTTGGAGGGGGTTCCATGTGTTAGTCAAGGAGGGGAACAGCAAAGTCACGGGAGCAGAGCTCA
GACAAGTCCTCACCACCCTGGGAGAGAAGATGGCTGAGGAGGAGATGGAGACTGTTCTGGCAGGACATGAGGACAGCATC
AACTAGGAGGCCTTCCTGAAACAC

Alignment

ORF - retro_nleu_369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.86 %
• Parental protein coverage: 93.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKPAGPSISKPAAKPAAAGAPPAKTKAEPAVPQAP--QKTQEPP-VDLSKVVIEFNKDQLEEFKEAFELF
          ..P..PSISK.AAKPAA..AP.A.TKAEP..P......K...PP.VDLSKVVI.FNKDQLEEFK.AF.LF
Retrocopy EEPTEPSISKAAAKPAATWAPLAMTKAEPVIPSPRHLRKPRSPP>VDLSKVVIKFNKDQLEEFKVAFKLF

Parental  DRVGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDELKSRRVDFETFLPMLQAVAKNRGQGTYEDY
          ..VGDGKILYSQ.GD.M..L.QN.T.A.V.KVLGNPKSDELKSR.VDF.TFLPMLQA.AK.R.QGTYEDY
Retrocopy N*VGDGKILYSQYGDMMGVLDQNLTSAKVMKVLGNPKSDELKSRHVDFKTFLPMLQAAAKKRNQGTYEDY

Parental  LEGL-RVFDKEGNGKVMGAELRHVLTTLGEKMTEEEVETVLAGHEDSNGCINYEAFLKH
          LEG...V..KEGN.KV.GAELR.VLTTLGEKM.EEE.ETVLAGHEDS...IN.EAFLKH
Retrocopy LEGV>HVLVKEGNSKVTGAELRQVLTTLGEKMAEEEMETVLAGHEDS---IN*EAFLKH

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_369 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000110	1 retrocopy	retro_cfam_1894,
Callithrix jacchus	ENSCJAG00000011620	3 retrocopies	retro_cjac_113, retro_cjac_2566, retro_cjac_2848,
Dasypus novemcinctus	ENSDNOG00000007592	1 retrocopy	retro_dnov_2073,
Homo sapiens	ENSG00000196465	1 retrocopy	retro_hsap_2383,
Gorilla gorilla	ENSGGOG00000003277	2 retrocopies	retro_ggor_1808, retro_ggor_2233,
Loxodonta africana	ENSLAFG00000012658	1 retrocopy	retro_lafr_734,
Macaca mulatta	ENSMMUG00000005214	1 retrocopy	retro_mmul_962,
Nomascus leucogenys	ENSNLEG00000000205	2 retrocopies	retro_nleu_2736, retro_nleu_779,
Nomascus leucogenys	ENSNLEG00000026948	1 retrocopy	retro_nleu_369 ,
Oryctolagus cuniculus	ENSOCUG00000017368	1 retrocopy	retro_ocun_374,
Otolemur garnettii	ENSOGAG00000001521	3 retrocopies	retro_ogar_1918, retro_ogar_3179, retro_ogar_680,
Procavia capensis	ENSPCAG00000005927	2 retrocopies	retro_pcap_223, retro_pcap_242,
Pongo abelii	ENSPPYG00000004646	1 retrocopy	retro_pabe_2150,
Pan troglodytes	ENSPTRG00000023043	2 retrocopies	retro_ptro_1741, retro_ptro_2579,
Rattus norvegicus	ENSRNOG00000028837	2 retrocopies	retro_rnor_1432, retro_rnor_216,