RetrogeneDB ID: retro_nleu_2235

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397336.1:10990747..10991403(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C7ORF42
• Ensembl ID: ENSNLEG00000013326
• Aliases: None
• Description: None

Sequence

>retro_nleu_2235
GCATCTACCAGGTCTTCCCAGGCCCTGGAGGATTCAGGCCCAGTTAACATCTCGGTCAAAATCACCCTAACCCTGGACCC
ACTCAAATTATTTGGATGCCATGATGCTCATGGCATCACTCATCTGTATTCAGTCATTTTAGGTCATCAGATTGGACTTT
CCGACAGAGAAGCCCACGAAGAGATAAATACTACCTTTTCTCTGCCTGAAGCTTGGACATCAGATAGCTGTGCTCTTGAT
GGTCACCATGAGCAGATGGTGTTCACAGCCTGCATGACCATCATGGACACCCCGGGTGTGTTCCCTGTCACTGTGCAGTC
ACCACACTGTGTTTCTGACACATACAGCAATGCCACAGTCTGGTGCAAGATCTTTAGAACTGACAGAAAGGCCAACACAG
AATACGCTCAAGATTACAGTCTTTTCTGGTGTTAGAAAAGGCCCATTGAAAAAGGCTATCATGCTTTTAATACCAAGCAT
AAGTTATCGCTCCAGATGATGACTGTTCATTAATAAATTTGCATCTCATGCATTCCAGTTACTTCCTCCTCACGATGGTG
ATAATAGTGTTTTGCTATACTGTTATCAAAGGCAGACCCAACAAACTGTGTCAGAGCAATCCTAAATATTATCCTGAGAA
GACAGCTTTGGCTGAA

Alignment

ORF - retro_nleu_2235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.18 %
• Parental protein coverage: 69.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASTQSPQALEDSGPVNISVAITLTLDPLKPFGGY-SRNVTHLYSTILGHQIGLSGREAHEEINITFTLPT
          AST.S.QALEDSGPVNISV.ITLTLDPLK.FG.......THLYS.ILGHQIGLS.REAHEEIN.TF.LP.
Retrocopy ASTRSSQALEDSGPVNISVKITLTLDPLKLFGCHDAHGITHLYSVILGHQIGLSDREAHEEINTTFSLPE

Parental  AWSSDDCALHGHCEQVVFTACMTLTASPGVFPVTVQPPHCVPDTYSNATLWYKIFTTARDANTKYAQDYN
          AW.SD.CAL.GH.EQ.VFTACMT....PGVFPVTVQ.PHCV.DTYSNAT.W.KIF.T.R.ANT.YAQDY.
Retrocopy AWTSDSCALDGHHEQMVFTACMTIMDTPGVFPVTVQSPHCVSDTYSNATVWCKIFRTDRKANTEYAQDYS

Parental  PFWCYKGAIGKVYHALNPKLT-VIVPDDDRSLINLHLMHTSYFLFVMVITMFCYAVIKGRPSKLRQSNPE
          .FWC.K..I.K.YHA.N.K...VI.PDDD.SLINLHLMH.SYFL..MVI..FCY.VIKGRP.KL.QSNP.
Retrocopy LFWC*KRPIEKGYHAFNTKHK<VIAPDDDCSLINLHLMHSSYFLLTMVIIVFCYTVIKGRPNKLCQSNPK

Parental  FCPEKVALAE
          ..PEK.ALAE
Retrocopy YYPEKTALAE

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_2235 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004278	1 retrocopy	retro_cjac_2145,
Cavia porcellus	ENSCPOG00000000830	1 retrocopy	retro_cpor_330,
Echinops telfairi	ENSETEG00000015971	1 retrocopy	retro_etel_2097,
Homo sapiens	ENSG00000106609	1 retrocopy	retro_hsap_3093,
Gorilla gorilla	ENSGGOG00000022776	1 retrocopy	retro_ggor_2124,
Myotis lucifugus	ENSMLUG00000000616	1 retrocopy	retro_mluc_1974,
Macaca mulatta	ENSMMUG00000015843	1 retrocopy	retro_mmul_1973,
Nomascus leucogenys	ENSNLEG00000013326	1 retrocopy	retro_nleu_2235 ,
Pan troglodytes	ENSPTRG00000019253	1 retrocopy	retro_ptro_2089,
Pteropus vampyrus	ENSPVAG00000002978	2 retrocopies	retro_pvam_988, retro_pvam_997,
Sorex araneus	ENSSARG00000001884	1 retrocopy	retro_sara_563,