RetrogeneDB ID: retro_nleu_2871

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397457.1:2144061..2144496(+)
• Located in intron of: ENSNLEG00000026810

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSRB2
• Ensembl ID: ENSNLEG00000012892
• Aliases: None
• Description: None

Sequence

>retro_nleu_2871
GAATTTCGGTCTCTTGCAACATGTGAGCTGCCTCTTGCCAAGAGTGAGTAGCAAAAGAAACTAAGCCCAGAGCAGTTCTG
TGTCGTGAGAGAAAAGGGAACAGAACCACCTTTCAGTGGGATCTACCTGAATAACAAGGAAGCAGGAATGTATCACTGTG
TGTGCTGCAATAGTCCACTCTTCAGTTTTGAGAAAAAGTACTGCTCCGGCACTGGGTGGCCTTCATTTGCTGAGGCTCAT
GGTATGTGTGGCTCTGATGAAAGCCACACAGGGATCCTGAGATGTCTGGACACCTCGTTAGGATCAGCTCACACAGAGGT
CGTCTGCAAGCAGTTTGAAGCTCATCTTGGTCACGTGGGTCCTGATGGACCCAGGCCCAATGGTCAGAGGTTTTGCATCA
ACAGTGTGGCTCTGAAGATCACACCAAGGAAACAT

Alignment

ORF - retro_nleu_2871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 79.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAESLATCELPLPKSEWQKKLTPEQFYVTREKGTEPPFSGIYLNNKEAGMYHCVCCDSPLFSSEKKYCSG
          E..SLATCELPL.KSE.QKKL.PEQF.V.REKGTEPPFSGIYLNNKEAGMYHCVCC.SPLFS.EKKYCSG
Retrocopy EFRSLATCELPLAKSE*QKKLSPEQFCVVREKGTEPPFSGIYLNNKEAGMYHCVCCNSPLFSFEKKYCSG

Parental  TGWPSFSEAHGTSGSDESHTGILRRLDTSLGSARTEVICKQCEAHLGHVFPDGPGPNGQRFCINSVALKF
          TGWPSF.EAHG..GSDESHTGILR.LDTSLGSA.TEV.CKQ.EAHLGHV.PDGP.PNGQRFCINSVALK.
Retrocopy TGWPSFAEAHGMCGSDESHTGILRCLDTSLGSAHTEVVCKQFEAHLGHVGPDGPRPNGQRFCINSVALKI

Parental  KPRKH
          .PRKH
Retrocopy TPRKH

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_2871 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006388	1 retrocopy	retro_amel_505,
Canis familiaris	ENSCAFG00000004215	1 retrocopy	retro_cfam_1147,
Equus caballus	ENSECAG00000013072	1 retrocopy	retro_ecab_593,
Nomascus leucogenys	ENSNLEG00000012892	1 retrocopy	retro_nleu_2871 ,
Pongo abelii	ENSPPYG00000002148	1 retrocopy	retro_pabe_3127,
Sus scrofa	ENSSSCG00000011077	1 retrocopy	retro_sscr_218,