RetrogeneDB ID: retro_nleu_815

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397273.1:27663500..27664253(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS5
• Ensembl ID: ENSNLEG00000010914
• Aliases: None
• Description: None

Sequence

>retro_nleu_815
GTGGTGACATCCAGGAGCGGTATGGTCCAAAAAACCTGGGAACTGGCCAACAACATGCAAGAAGCTCAGAGTATCCATGA
AGGCTACAAATACGACAAGAAGCAGCAGCATGAAATCCTGGCAGCAAAGCCCTGTGTTAACAATCACCATTACTTTAAAG
TACTGCAAAATCTCAGCATTAGCTCTACTGAAGATGATGATGCATGCCAGATCAGAGGGCAACTTGGAAGTGATGCGTTT
GATGCCAGGAAAGGTAGATGGTGAAACCACGATTATTATGGGCAGTTTTACTTTGCCTGTGGAGGGCACTGAAACCCGAG
AAAATGCTCCGGCTGCTGCATGTGAGTGCGTGGCCACATACATAGAAAATGCCAAAAAGGTTGGCCGCCTTAAAAATGCA
ATCGGATGGTATTATAGGCACCCTGGCCATGGCTGCTGGCTTTCTGACATCATGTTAGTACTCAGCTGCTCAATAAGTGG
TTCCGGGAACCATTTTCGGCAGTGGTGATTGATCCAACAAGAACAATATCTGCAGGGAAAGTGAATCTTGATGCCTTTAG
GACATACCCAAAGGGCTACAAACCTCCTGATGAAGGACCTTCTGAGTACCAGACTATCCCGCTTAATAAAATAGAAGATG
TTGTTGTACAATGCAAACAATATTATGTCTTAGAAGTCTTGTATTTCAAATTCTCTTTGGGTTGCAAATTGCTTGAGCTT
CTGTGGAATAAATATTGGGTGGGTACACTGAGT

Alignment

ORF - retro_nleu_815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.63 %
• Parental protein coverage: 75.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFK-YCKISALALLKMVMHA
          ...S.SGM.QKTWELANNMQEAQSI.E.YKYDKKQQ.EILAAKP....HHYFK.YCKISALALLKM.MHA
Retrocopy VVTSRSGMVQKTWELANNMQEAQSIHEGYKYDKKQQHEILAAKPCVNNHHYFK>YCKISALALLKMMMHA

Parental  RSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHS
          RS.GNLEVM.LM.GKVDGET.IIM.SF.LPVEGTETR.NA.AAA.E..A.YIENAK.VGRL.NAIGWY..
Retrocopy RSEGNLEVMRLMPGKVDGETTIIMGSFTLPVEGTETRENAPAAACECVATYIENAKKVGRLKNAIGWYYR

Parental  HPGYGCWLSGI-DVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPL
          HPG.GCWLS.I..VSTQ.LN..F.EPF.AVVIDPTRTISAGKVNL.AFRTYPKGYKPPDEGPSEYQTIPL
Retrocopy HPGHGCWLSDI<HVSTQLLNKWFREPFSAVVIDPTRTISAGKVNLDAFRTYPKGYKPPDEGPSEYQTIPL

Parental  NKIEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLS
          NKIED..V.CKQYY.LEV.YFK.SL..KLLELLWNKYWV.TLS
Retrocopy NKIEDVVVQCKQYYVLEVLYFKFSLGCKLLELLWNKYWVGTLS

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_815 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004632	1 retrocopy	retro_cjac_2454,
Homo sapiens	ENSG00000121022	1 retrocopy	retro_hsap_3634,
Microcebus murinus	ENSMICG00000011042	1 retrocopy	retro_mmur_834,
Monodelphis domestica	ENSMODG00000007838	1 retrocopy	retro_mdom_1460,
Mustela putorius furo	ENSMPUG00000010175	1 retrocopy	retro_mputfur_397,
Nomascus leucogenys	ENSNLEG00000010914	1 retrocopy	retro_nleu_815 ,
Pongo abelii	ENSPPYG00000018648	1 retrocopy	retro_pabe_2980,
Pan troglodytes	ENSPTRG00000020317	2 retrocopies	retro_ptro_2457, retro_ptro_638,