RetrogeneDB ID: retro_nleu_1373

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397291.1:24635803..24636216(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAGE3
• Ensembl ID: ENSNLEG00000014285
• Aliases: None
• Description: L antigen family, member 3 [Source:HGNC Symbol;Acc:26058]

Sequence

>retro_nleu_1373
ATGCAGACGCAGGCGGAGGCGCCAACTGCGGGGATGGCCAGGGTGATCACAGCTGCCCCGGGGCCGCCGACACCCCGGCA
GCTCCGGCCAGCGGAGCTCCCCCACCGCACCCGTCAGATCCTGGCAGAGGCGCCGCGTCTGTGGCCAGGGGGCCGGGAAT
GCGGCCGCACATATTCACCCTCAGCGTGCCTTTCCCGACCCCCTTAGAGGCGGAAATTGCCCATGGGTCCCTGGCTCCAG
ATGCCGAGCCCCACCAAAGGGTGGTTCGGCGGGATCTCACAGTGAGCGGCAGGATCCTGGCCGTCCGCTGGAAAGCTGAA
GACTGTCGCCTGCTCCGAATTTCCGTTATCAACTTTCTTGACCATCTTTCTCTGGTGGTGCGGACCCTGCAGCACTTTGG
GACCCCCGTTTCC

Alignment

ORF - retro_nleu_1373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.17 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQTQAEAPTAGMA-QGGHSCPGGADTAAAPAGGAPPAHAPGPGRDAASAARGSGVRPHIFTLSVPFPTLL
          MQTQAEAPTAGMA.QG.HSCPG.ADT.AAPA.GAPP.H...PGR.AAS.ARG.G.RPHIFTLSVPFPT.L
Retrocopy MQTQAEAPTAGMA<QGDHSCPGAADTPAAPASGAPPPHPSDPGRGAASVARGPGMRPHIFTLSVPFPTPL

Parental  EAEIAHGSLAPDAEPHQRVVGKDLTVSGRILVVRWKAEDCRLLRISVINFLDQLSLVLRTMQRFGPPVS
          EAEIAHGSLAPDAEPHQRVV..DLTVSGRIL.VRWKAEDCRLLRISVINFLD.LSLV.RT.Q.FG.PVS
Retrocopy EAEIAHGSLAPDAEPHQRVVRRDLTVSGRILAVRWKAEDCRLLRISVINFLDHLSLVVRTLQHFGTPVS

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_1373 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024143	1 retrocopy	retro_dnov_244,
Dipodomys ordii	ENSDORG00000009093	1 retrocopy	retro_dord_448,
Homo sapiens	ENSG00000196976	1 retrocopy	retro_hsap_4244,
Gorilla gorilla	ENSGGOG00000013507	1 retrocopy	retro_ggor_2845,
Macaca mulatta	ENSMMUG00000007739	1 retrocopy	retro_mmul_1145,
Mus musculus	ENSMUSG00000015289	2 retrocopies	retro_mmus_1411, retro_mmus_1665,
Nomascus leucogenys	ENSNLEG00000014285	1 retrocopy	retro_nleu_1373 ,
Ochotona princeps	ENSOPRG00000003778	2 retrocopies	retro_opri_196, retro_opri_549,
Pongo abelii	ENSPPYG00000020881	1 retrocopy	retro_pabe_3394,
Rattus norvegicus	ENSRNOG00000037249	1 retrocopy	retro_rnor_595,
Sus scrofa	ENSSSCG00000025528	1 retrocopy	retro_sscr_94,