RetrogeneDB ID: retro_nleu_1548

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397298.1:21090566..21091105(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRR3
• Ensembl ID: ENSNLEG00000005104
• Aliases: None
• Description: None

Sequence

>retro_nleu_1548
AATCAGCACCAGCCCCCGCCACAGCAGCAGCCCCCACTGCCCAAGAGGGAAAAGACTGGAGATGACGAGGATGGGAGTCC
CATCGGATCACCCAGCCTTCTGAGCCTCCCCTATGGCCAGTGGAAAACCTGATGACCCTAAGTCAGCTCCTCACAGAAGT
CCTCCAGGAGCAAGGGAATCACTGATTCCACCACTGCTGAGCCTCCCACCTCCTCCTCAGGGTAGAGGCCCAGTGCCAGG
AGGCCTTGGCCCCAGGCCTAACCCATATAATTGTGGTTGGTGGGGAGTCAATGCTGAACCTCCTTTTCCGGGGCCAGGTC
ATGGGGGTCCCGCCAGGCGAAGCCTTCACAAAGAACAGAGAAACCCTCAAAGGCTCTAAAGCTGGTCTCTTATCAAGAAT
ACCAGCCCACTAGGATGACCCCCAGGTTATGGAAGACAAATCCCACCACCTAGTCTGTGGACATTTTGCCAAAAAGGGCC
ACTGTTGATATGAGGACCTCTGTGCCTTCCACCACCCAGGCATCAATAGCCCTCCTCTG

Alignment

ORF - retro_nleu_1548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.57 %
• Parental protein coverage: 71.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NQHQPPTQQQPPLPEREETGDEEDGSPIGPPSLLG-PP-PMANGKPGDPKSALHRGPPGSRGPLIPPLLS
          NQHQPP.QQQPPLP.RE.TGD.EDGSPIG.PSLL..PP.PMA.GKP.DPKSA.HR.PPG.R..LIPPLLS
Retrocopy NQHQPPPQQQPPLPKREKTGDDEDGSPIGSPSLLS<PP<PMASGKPDDPKSAPHRSPPGARESLIPPLLS

Parental  LPPPPWGRGPIRRGLGPRSSPYGRGWWGVNAEPPFPGPGHGG-PTRGSFHKEQRNPRRLKSWSLIKNTCP
          LPPPP.GRGP...GLGPR..PY..GWWGVNAEPPFPGPGHGG.P....F.K........K...L......
Retrocopy LPPPPQGRGPVPGGLGPRPNPYNCGWWGVNAEPPFPGPGHGG>PPGEAFTKNRETLKGSKA-GLLSRIPA

Parental  PKDDPQVMEDKSDRPVCRHFAKKGHCRYEDLCAFYHPGVNGPPL
          ..DDPQVMEDKS...VC.HFAKKGHC.YEDLCAF.HPG.N.PPL
Retrocopy H*DDPQVMEDKSHHLVCGHFAKKGHC*YEDLCAFHHPGINSPPL

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_1548 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022770	1 retrocopy	retro_cpor_775,
Felis catus	ENSFCAG00000025918	2 retrocopies	retro_fcat_1094, retro_fcat_1698,
Gorilla gorilla	ENSGGOG00000014604	1 retrocopy	retro_ggor_1915,
Myotis lucifugus	ENSMLUG00000008758	1 retrocopy	retro_mluc_1567,
Macaca mulatta	ENSMMUG00000013893	1 retrocopy	retro_mmul_1431,
Nomascus leucogenys	ENSNLEG00000005104	1 retrocopy	retro_nleu_1548 ,
Otolemur garnettii	ENSOGAG00000004430	2 retrocopies	retro_ogar_1030, retro_ogar_1324,
Pongo abelii	ENSPPYG00000016409	1 retrocopy	retro_pabe_2279,
Pan troglodytes	ENSPTRG00000017929	1 retrocopy	retro_ptro_1861,
Sorex araneus	ENSSARG00000002747	2 retrocopies	retro_sara_143, retro_sara_9,
Ictidomys tridecemlineatus	ENSSTOG00000011829	1 retrocopy	retro_itri_126,
Tarsius syrichta	ENSTSYG00000000166	2 retrocopies	retro_tsyr_308, retro_tsyr_841,