RetrogeneDB ID: retro_nleu_1556

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397299.1:10812506..10813093(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GYG1
• Ensembl ID: ENSNLEG00000002557
• Aliases: None
• Description: None

Sequence

>retro_nleu_1556
ATTTATCAGCCTTCAGTTGAAACATATAATCAGCTGTTGCATCTTGCTTCTGAGCAAGGTAGTTTTGATGGTGGGGAACA
AGGCATATGGAACACATTTTTTCACAGCTGGGCAACAACAGATATCAGAAAACACCTGCCATTTATTTATAGCCTAAGCC
ACATCTCTATATAGTCCTACCTCCCAGCATTTAAAGTGTTTGGTGCAAGTGCCAAAGTCGTGCATTTCCTGGGACGAGTC
AAACCATGGAATTATACTTATGATCCCAAAACAAAAAGTGTCAAAAATGAGTCCCACCATCCCAACGTGACTCATCGAGA
GTTTCTCATCCTGTGGTGGAACATCTTTACCACCAAAGTTTTACCTCTGCTTGAACAATTTGGCCTTGTCAAAGACACCT
GCTCATATGTAAATGTGGAAGATGTCTCAGGAGCCGTATCACATCTGTCCCTTGGGGAGATCCCAGCTATGGCACAGCCT
TTGTATCCTCAGAAGAACAGAAGGAGCAGTGGGAACAGGGCTAGACTGATTATATGGGAGCAGATTCCTTTGACAACATC
AAGAGGAAACTTGACGCTTACCTCCAG

Alignment

ORF - retro_nleu_1556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.82 %
• Parental protein coverage: 58.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VYQPSLETYNQLLCLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGAG
          .YQPS.ETYNQLL.LASEQGSFDGG.QGI.NTFF.SWATTDIRKHLPFIY.LS.ISI.SYLPAFKVFGA.
Retrocopy IYQPSVETYNQLLHLASEQGSFDGGEQGIWNTFFHSWATTDIRKHLPFIYSLSHISI*SYLPAFKVFGAS

Parental  AKVVHFLGRVKPWNYTYDPKTKSVKSEAHDPNMTHPEFLILWWNIFTTNVLPLLQQFGLVKDTCSYVNVE
          AKVVHFLGRVKPWNYTYDPKTKSVK.E.H.PN.TH.EFLILWWNIFTT.VLPLL.QFGLVKDTCSYVNVE
Retrocopy AKVVHFLGRVKPWNYTYDPKTKSVKNESHHPNVTHREFLILWWNIFTTKVLPLLEQFGLVKDTCSYVNVE

Parental  DVSGAISHLSLGEIPAMAQP-FVSSEERKERWEQGQADYMGADSFDNIKRKLDTYLQ
          DVSGA.SHLSLGEIPAMAQP.FVSSEE.KE.WEQG..DYMGADSFDNIKRKLD.YLQ
Retrocopy DVSGAVSHLSLGEIPAMAQP<FVSSEEQKEQWEQG*TDYMGADSFDNIKRKLDAYLQ

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_1556 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001467	2 retrocopies	retro_cjac_1049, retro_cjac_2915,
Danio rerio	ENSDARG00000011934	1 retrocopy	retro_drer_23,
Homo sapiens	ENSG00000163754	2 retrocopies	retro_hsap_1222, retro_hsap_159,
Myotis lucifugus	ENSMLUG00000006382	1 retrocopy	retro_mluc_2351,
Macaca mulatta	ENSMMUG00000005521	2 retrocopies	retro_mmul_1297, retro_mmul_376,
Nomascus leucogenys	ENSNLEG00000002557	2 retrocopies	retro_nleu_1556 , retro_nleu_693,
Oryctolagus cuniculus	ENSOCUG00000003516	1 retrocopy	retro_ocun_1766,
Pongo abelii	ENSPPYG00000025899	2 retrocopies	retro_pabe_1015, retro_pabe_1080,
Pan troglodytes	ENSPTRG00000015509	1 retrocopy	retro_ptro_836,