RetrogeneDB ID: retro_nleu_3005

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397567.1:559230..559762(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000026297
• Ensembl ID: ENSNLEG00000011573
• Aliases: None
• Description: None

Sequence

>retro_nleu_3005
ATGGTCCAGCACTGGCCTGAGACAGTATGCGAGAAAGTTCAAAACGACGGTAGAGACCCTCCGGATTACTGGACAATACA
TGGGACTATTGCCCGATAAAAGTGAAGGATGTAATGGATTGTGGCACTTTAATTTAGAAGAGATTAAAGATCTTTTGCCG
GAAATGAAGGCATACTGGCCTGATGTAATTCACTCATTTCCCAGTCGTAGCCACTTCTGGAAGCATGAGTGGGAGAAGCA
TGGGACCTGTGCCGCCCTGGTGGACGCACTCAACTCCCAGAAGCAGTACTTTAGCAGAAGCCTGGAACTCTACAGGGAGC
TGGAACGCAACAGTGTGCTTCTAAAACTGCGGCTAAAACCATCCATCAATTACTACCAAGTTGCAGGTTTTAAAGATGCC
CTTGTCAGAGTGTATGGAGTGATACGCAAAATCCAGTGCCTTCTGCGAAGCCAGGATGGGGAAGTACAGACAATTGGTCA
GACAGAACTTTGCCTCACTGAGCAAGGCCAGTAGCTGCAAAACTGCACCGAG

Alignment

ORF - retro_nleu_3005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.83 %
• Parental protein coverage: 81.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVQHWPETVCEEIQNDCRDPPDYWTIHG-LWPDKSEGCNRSWPFNLEEIKDLLPEMKAYWPDVIHSFPNR
          MVQHWPETVCE..QND.RDPPDYWTIHG.L.PDKSEGCN..W.FNLEEIKDLLPEMKAYWPDVIHSFP.R
Retrocopy MVQHWPETVCEKVQNDGRDPPDYWTIHG>LLPDKSEGCNGLWHFNLEEIKDLLPEMKAYWPDVIHSFPSR

Parental  SRFWKHEWEKHGTCAAQVDALNSQKKYFGRSLELYRELDLNSVLLKLGIKPSINYYQVADFKDALARVYG
          S.FWKHEWEKHGTCAA.VDALNSQK.YF.RSLELYREL..NSVLLKL..KPSINYYQVA.FKDAL.RVYG
Retrocopy SHFWKHEWEKHGTCAALVDALNSQKQYFSRSLELYRELERNSVLLKLRLKPSINYYQVAGFKDALVRVYG

Parental  VIPKIQCLPPSQDEEVQTIGQIELCLTKQDQQLQNCTE
          VI.KIQCL..SQD.EVQTIGQ.ELCLT.Q.Q.LQNCTE
Retrocopy VIRKIQCLLRSQDGEVQTIGQTELCLTEQGQ*LQNCTE

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_3005 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000003359	1 retrocopy	retro_lafr_764,
Microcebus murinus	ENSMICG00000014184	1 retrocopy	retro_mmur_1544,
Macaca mulatta	ENSMMUG00000005673	1 retrocopy	retro_mmul_1684,
Monodelphis domestica	ENSMODG00000006193	1 retrocopy	retro_mdom_1994,
Nomascus leucogenys	ENSNLEG00000011573	1 retrocopy	retro_nleu_3005 ,
Pongo abelii	ENSPPYG00000017277	1 retrocopy	retro_pabe_3128,
Pan troglodytes	ENSPTRG00000018796	1 retrocopy	retro_ptro_2529,