RetrogeneDB ID: retro_nleu_2045

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397324.1:4620379..4620995(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL9
• Ensembl ID: ENSNLEG00000010275
• Aliases: None
• Description: None

Sequence

>retro_nleu_2045
TGGAAGGTACCAATGGCCGGGGAGGGCCAGAAGCTGCGCCTGCACCAGCGACACTACATCCACAAGCTGGTGGAGGACAC
GAAGCACTGGCTCAAAGAAAACCTGGAGATCATCTTCACACAGTCTGTGGAGACACTTGGAGTCCGGGGTGACCTGGTCT
CAGTAAAGAAATCTGTGGATCAGAATCAACTCCTTCCTCAGAGACTGGCTGCATATGTATCATCTGAAAACAAGAAGCTG
TTTGAAGAGGAGAAATTGCTGAGACCAGGAGGAAAGTTAGAGAAGATCCAGATCAAGGCAGGTGAGGCAACAGTGACATT
TCTGAATAGCTGTCACTTGGAGGTAGGGATGAAGAACAATGTCAAATGGGAGCTGAACCCTGAAACAGTTGCCCACCACT
TCTTCAAGAATCTTGGTGTTGTGGTCACCCCCCATACATTAAAGTTACCAGAAGAGCCCCTCATTCGGTGGGGCAAGTAC
TGGTGTGAGGTGATGGTAAATGGGCTTGGTACTGTGAGGGTGCCTATGTCTCTGGTAAACCTTGAGAGGCCCAAAATCAA
AAGATAGAAGTACTGGTTACCCAGCAAGCTGCCAAGGGCATGGCCCTACCAGCCCC

Alignment

ORF - retro_nleu_2045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.37 %
• Parental protein coverage: 77.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WKVPLAGEGRKPRLHRRHRVYKLVEDTKHRPKENLELILTQSVENVGVRGDLVSVKKSLGRNRLLLQGLA
          WKVP.AGEG.K.RLH.RH...KLVEDTKH..KENLE.I.TQSVE..GVRGDLVSVKKS...N.LL.Q.LA
Retrocopy WKVPMAGEGQKLRLHQRHYIHKLVEDTKHWLKENLEIIFTQSVETLGVRGDLVSVKKSVDQNQLLPQRLA

Parental  VYASPENKKLFEEEKLLRQEGKLEKIQTKAGEATVKFLKSCRLEVGMKNNVKWELNPEIVARHFFKNLGV
          .Y.S.ENKKLFEEEKLLR..GKLEKIQ.KAGEATV.FL.SC.LEVGMKNNVKWELNPE.VA.HFFKNLGV
Retrocopy AYVSSENKKLFEEEKLLRPGGKLEKIQIKAGEATVTFLNSCHLEVGMKNNVKWELNPETVAHHFFKNLGV

Parental  VVAPHTLKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVNFEKPKTKRYKYWL-AQQAAKAMA-PTSP
          VV.PHTLKLPEEP..RWG.YWCEV.VNGL.TVRVPMS.VN.E.PK.KR.KYWL..QQAAK.MA.PTSP
Retrocopy VVTPHTLKLPEEPLIRWGKYWCEVMVNGLGTVRVPMSLVNLERPKIKR*KYWL<TQQAAKGMA<PTSP

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_2045 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989,
Homo sapiens	ENSG00000143436	1 retrocopy	retro_hsap_4078,
Gorilla gorilla	ENSGGOG00000001902	1 retrocopy	retro_ggor_2735,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498, retro_lafr_563,
Nomascus leucogenys	ENSNLEG00000010275	1 retrocopy	retro_nleu_2045 ,
Oryctolagus cuniculus	ENSOCUG00000001383	1 retrocopy	retro_ocun_725,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Pongo abelii	ENSPPYG00000000857	1 retrocopy	retro_pabe_3347,
Pan troglodytes	ENSPTRG00000001295	2 retrocopies	retro_ptro_2765, retro_ptro_2996,