RetrogeneDB ID: retro_nleu_2850

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397451.1:994875..995581(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000005243
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSNLEG00000012195
• Aliases: None
• Description: None

Sequence

>retro_nleu_2850
ATGGCAATTACAAAATTTGATCAATTTGATTTTCTCATCGATATTGTTCTAAGAGATGAACTGAAACCTCCAAAGTGTCA
GGAGGAGGTGCTGCAGTCTGTAACTCCTGCTAAGCCAGTCCAGTACTATTTCACACTGGCTCAGCAGCCCACCGCCGTCC
AAGTCCAGGGGCAGCAGTAAGGCCAGCCCACCGCCAGCTCCATGACCACCATCCAGCCTGGGCAGATCATCATCGCACAG
CCTCAGCAGGGCCAGACCACGCCCGTGACAACGCAGGTTGGAGAAGGTCAGCAGGTGCAGATTGTCCAGGCCCAGGCACA
GGGTCAAGCCCAATAGGCCCAGAGTGGTACTGGATGGACCGTGCAGGTGATGCAGCAGATCCTCACTAACACAGGAGAGA
TCTAGCAGATCCCAGTGCAGCTGAAAGTTGGCCAGCTGCAGTGTATCGGCTTAGCCCGGTCTGTATCAGGCACCCGAGTT
CTGCAGGGACAGATCCAGACACTTGCCACCAGCGCTCAACCGATTACACAGGCAGAGGTCCAGCAAAGACAGCAGTAGTT
CAGCCAGTTCACAGATGGACAGCAGCTCTACCAGATCTAGCAAGGAACCATACCTGCGGGCCAGGACCTGCCCAGCCCAT
GTTTATCCAGTCAGTCAACCAGCCCTCCGATGGGCAGGCCCCCCAGGTGACTGGCGACTGAGGGCC

Alignment

ORF - retro_nleu_2850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTT
          MAITKFDQFDFLIDIV.RDELKPPK.QEEV.QSVTPA.PVQYYFTLAQQPTAVQVQGQQ.GQ.T.SS.TT
Retrocopy MAITKFDQFDFLIDIVLRDELKPPKCQEEVLQSVTPAKPVQYYFTLAQQPTAVQVQGQQ*GQPTASSMTT

Parental  IQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQ
          IQPGQIIIAQPQQGQTTPVT.QVGEGQQVQIVQAQ.QGQAQ.AQSGTG.T.QVMQQI.TNTGEI.QIPVQ
Retrocopy IQPGQIIIAQPQQGQTTPVTTQVGEGQQVQIVQAQAQGQAQ*AQSGTGWTVQVMQQILTNTGEI*QIPVQ

Parental  LNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQITQTEVQQGQQQFSQFTDGQQLYQIQQVTMRA-RTS
          L..GQLQ.I.LA..VSGT.V.QGQIQTLAT.AQ.ITQ.EVQQ.QQ.FSQFTDGQQLYQI.Q.T..A....
Retrocopy LKVGQLQCIGLARSVSGTRVLQGQIQTLATSAQPITQAEVQQRQQ*FSQFTDGQQLYQI*QGTIPAGQDL

Parental  PSPCSSSQPTSPPTG-PP-GDRRLRA
          PSPC.SSQ.TSPP.G.PP.GD.RLRA
Retrocopy PSPCLSSQSTSPPMGRPP>GDWRLRA

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_2850 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012591	1 retrocopy	retro_acar_33,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050,
Nomascus leucogenys	ENSNLEG00000001111	1 retrocopy	retro_nleu_670,
Nomascus leucogenys	ENSNLEG00000012195	2 retrocopies	retro_nleu_2369, retro_nleu_2850 ,
Pongo abelii	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,