RetrogeneDB ID: retro_nleu_3086

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397901.1:16843..17299(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME2
• Ensembl ID: ENSNLEG00000015260
• Aliases: None
• Description: None

Sequence

>retro_nleu_3086
GTCCCTAAGTGTGGATTTCTCCCTGGGAATGAGAAGGTCCTGTTCCTGCTTGTCCTGGTTAAGCCGGAAGTCTGGAGTCT
CAAAGAGAAATGCATTCTGGTGATCACATGGATCCAGCACCTGATCCTCAAGATTGAAGTTGGAAATGATTTTGGAGTAG
CAATCCAGGAGAAGGTGCTGGAGAGGGTGAATGCCATCAAGAGCAAAGTGGAAGCTTTCCAGACAACCATTTCCAAGTAC
TTCTCAGAATGTCAGGATGCCGTGGCCAAGGCCTCTAAGGAGACTCATGTAATGGACTACCAGGTCTTGGTGCACCAGTG
AGATGAGGCAGCCTATGGGGAGCTCAGGGCCATGGTGCTGGACTTCAGAGCCTTCTACGCTGAGGTTTATCATATCAGCA
GCAGCAACCCGGAGAAAATTGTCAACCCAAAGGGTGAAGAGAAGCCATCTATGCAC

Alignment

ORF - retro_nleu_3086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.16 %
• Parental protein coverage: 59.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPKCGFLPGNEKVLSLLALVKPEVWTLKEKCILVITWIQHLIPKIEDGNDFGVAIQEKVLERVNAVKTKV
          VPKCGFLPGNEKVL.LL.LVKPEVW.LKEKCILVITWIQHLI.KIE.GNDFGVAIQEKVLERVNA.K.KV
Retrocopy VPKCGFLPGNEKVLFLLVLVKPEVWSLKEKCILVITWIQHLILKIEVGNDFGVAIQEKVLERVNAIKSKV

Parental  EAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVLDLRAFYAELYHIISSNLEKI
          EAFQTTISKYFSE..DAVAKASKETHVMDY..LVH..DEAAYGELRAMVLD.RAFYAE.YHI.SSN.EKI
Retrocopy EAFQTTISKYFSECQDAVAKASKETHVMDYQVLVHQ*DEAAYGELRAMVLDFRAFYAEVYHISSSNPEKI

Parental  VNPKGEEKPSMY
          VNPKGEEKPSM.
Retrocopy VNPKGEEKPSMH

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_3086 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 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233, retro_cjac_322, retro_cjac_71,
Homo sapiens	ENSG00000100911	4 retrocopies	retro_hsap_1200, retro_hsap_2999, retro_hsap_3033, retro_hsap_3222,
Gorilla gorilla	ENSGGOG00000016025	4 retrocopies	retro_ggor_2078, retro_ggor_2093, retro_ggor_2188, retro_ggor_935,
Macaca mulatta	ENSMMUG00000012473	4 retrocopies	retro_mmul_1229, retro_mmul_1919, retro_mmul_1940, retro_mmul_2281,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145,
Nomascus leucogenys	ENSNLEG00000015260	4 retrocopies	retro_nleu_2086, retro_nleu_2726, retro_nleu_3086 , retro_nleu_844,
Otolemur garnettii	ENSOGAG00000016584	1 retrocopy	retro_ogar_61,
Pongo abelii	ENSPPYG00000005684	4 retrocopies	retro_pabe_1000, retro_pabe_2486, retro_pabe_2512, retro_pabe_2669,
Pan troglodytes	ENSPTRG00000006196	4 retrocopies	retro_ptro_2028, retro_ptro_2046, retro_ptro_2172, retro_ptro_820,