RetrogeneDB ID: retro_nleu_173

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:30143920..30144581(+)
• Located in intron of: ENSNLEG00000016158

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIL4
• Ensembl ID: ENSNLEG00000015316
• Aliases: None
• Description: None

Sequence

>retro_nleu_173
GCCTGCTTTAATTTCTTGAGATATTACAAAATAAAATATTACAGTTATTGCCTTATTCACAGTGTACGAAGGTATTTTAT
CATACAAACTGTTGATCCTACAGGGACTGGTCATGGAGGAGAGTCTATTTTTGGCCAATTGTATGGTGATCAAGCAAGCT
TTTTTGAGACAGAAAACGTCCCAAGAATTAAGCATAAGAAGAAAGACACAATGTCCATGGTGAACAATGGCAGTGATCAA
CATGGATCTCAGTTTCTTATCACTACAGGAGAAAAATCTAGATTACCTTGATGGTACCATACAGTATTTGGTGAGGTGAC
AGAAGGCATTGACATAATTAAGAAAATTAATGAGACCTTTGTTGACAAGGACTTTGTACCATATCAGGATATCAGGATAA
ATTATACAGTGATTTTAGATGGTCCATTTTGATGACATTCCTGATTTATTAATCCCTGATCGATCACCAGAACCTACAAG
GGAACAATTAAAGAGTGGTAGAATTGACGCAGATGAAGAAATTGATCATTTCAAAGGAAGGTCAGCCGAAGAAGTAGAAG
AAATAAAGGCAGAAAAAGAAGCTAAAACTCAGGCTTTACTTTTAGAGATGGTGGGAGACCTACCTGATGCAGATATTAAA
CCTCCAGAAAAATCTGTATAT

Alignment

ORF - retro_nleu_173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 51.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTGRGGESIFGQLYGDQASFFEAEKVPRIKHKKKGT
          AC.NFL...KIKYY.YCLIH.V.R.FIIQT.DPTGTG.GGESIFGQLYGDQASFFE.E.VPRIKHKKK.T
Retrocopy ACFNFLRYYKIKYYSYCLIHSVRRYFIIQTVDPTGTGHGGESIFGQLYGDQASFFETENVPRIKHKKKDT

Parental  VSMVNNGSDQHGSQFLITTGE-NLDYLDGV-HTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVI
          .SMVNNGSDQHGSQFLITTGE.NLDYLDG..HTVFGEVTEG.DIIKKINETFVDKDFVPYQDIRIN.TVI
Retrocopy MSMVNNGSDQHGSQFLITTGE>NLDYLDGT<HTVFGEVTEGIDIIKKINETFVDKDFVPYQDIRINYTVI

Parental  LDDP-FDDPPDLLIPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDL
          LD.P.FDD.PDLLIPDRSPEPTREQL.SGRI.ADEEID.FKGRSAEEVEEIKAEKEAKTQA.LLEMVGDL
Retrocopy LDGP>FDDIPDLLIPDRSPEPTREQLKSGRIDADEEIDHFKGRSAEEVEEIKAEKEAKTQALLLEMVGDL

Parental  PDADIKPPENVLF
          PDADIKPPE....
Retrocopy PDADIKPPEKSVY

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_173 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019613	1 retrocopy	retro_cjac_2963,
Macaca mulatta	ENSMMUG00000023067	1 retrocopy	retro_mmul_1715,
Nomascus leucogenys	ENSNLEG00000010779	1 retrocopy	retro_nleu_2135,
Nomascus leucogenys	ENSNLEG00000012313	2 retrocopies	retro_nleu_1242, retro_nleu_289,
Nomascus leucogenys	ENSNLEG00000015316	1 retrocopy	retro_nleu_173 ,
Oryctolagus cuniculus	ENSOCUG00000007696	2 retrocopies	retro_ocun_661, retro_ocun_892,
Taeniopygia guttata	ENSTGUG00000010655	1 retrocopy	retro_tgut_16,