RetrogeneDB ID: retro_nleu_2542

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397369.1:4518762..4519310(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOMM40
• Ensembl ID: ENSNLEG00000001726
• Aliases: None
• Description: None

Sequence

>retro_nleu_2542
ATGGGGAACGTGTTGGCAGTCAGCTTGCTGCCTGCAGGGCAGCCGCCACCACCTGTGCCGGCGCTCGTGGGACTGCCGCC
ACCTCCGCCCTAGCATCCAGGCTTCACGCTGCCGCCGCTGGGAGGCGGCCTGGGCGCCAGCACCAGTGAGGGTCGAGGTT
TGGAGCGGACCCCGGAGCTGCAACCGCCAGTGCCGCAGGGGGTGCCGAGGATGGGGCCTGCCGCTGCCTGCCCTACCCCT
GCACATTCAAGGAGTGCTACCGGAAGTACAAGGAGCTGTAGATGGAAGGTGTCAAGTTCACAGTGAACAAAGCGTTGAGT
AAGCATTTCCAGGTAAACCACACAGTAACCCTCAGCACAATCAGGGAGTCCAACAACCATTTTGGTGTCACGTATATGGG
GACAAAGCAGCTGAGTCCCACAGAGGCATTCCCTGTACTGGTGGGTGACATGGACAACAGTGGCAGCCTCAATGCTCAGG
TCATTCACCAGCTGGGCCCCGGCCTCAGGTCCAAGATGGCCATACAGACCCAGCAGTCGAAGTTTGTG

Alignment

ORF - retro_nleu_2542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 56.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRGSERTP-GAATASASGAA
          MGNVLA.S..PAG.PPPP.PALVGLPPPPP..PGFTLPPLGG.LGA.TS..RG.ERTP.GAATASA.G.A
Retrocopy MGNVLAVSLLPAGQPPPPVPALVGLPPPPP*HPGFTLPPLGGGLGASTSEGRGLERTP<GAATASAAGGA

Parental  EDGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTK
          EDGAC.CLP.P.TF.EC.RK.KE.....MEGVK.TVNK.LS.HFQVNHTV.LSTI.ESN.HFGVTY.GTK
Retrocopy EDGACRCLPYPCTFKECYRKYKE---L*MEGVKFTVNKALSKHFQVNHTVTLSTIRESNNHFGVTYMGTK

Parental  QLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFV
          QLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFV
Retrocopy QLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFV

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_2542 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130204	5 retrocopies	retro_hsap_1300, retro_hsap_1386, retro_hsap_2321, retro_hsap_2537, retro_hsap_3159,
Gorilla gorilla	ENSGGOG00000023033	1 retrocopy	retro_ggor_1356,
Microcebus murinus	ENSMICG00000014041	1 retrocopy	retro_mmur_420,
Myotis lucifugus	ENSMLUG00000028928	1 retrocopy	retro_mluc_697,
Nomascus leucogenys	ENSNLEG00000001726	2 retrocopies	retro_nleu_2368, retro_nleu_2542 ,
Oryctolagus cuniculus	ENSOCUG00000023582	1 retrocopy	retro_ocun_1143,
Pongo abelii	ENSPPYG00000025858	1 retrocopy	retro_pabe_174,
Pan troglodytes	ENSPTRG00000011126	1 retrocopy	retro_ptro_39,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,