RetrogeneDB ID: retro_nleu_818

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397273.1:35471771..35472989(-)
• Located in intron of: ENSNLEG00000013890

Retrocopy information

• Ensembl ID: ENSNLEG00000013981
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VMP1
• Ensembl ID: ENSNLEG00000000724
• Aliases: None
• Description: None

Sequence

>retro_nleu_818
ATGGCAGAGAATGGAAAAAATTGTGACCAGAGACGTGTAGCAATGAACAAGGAACAACATAATGGAAATTTCACAGACCT
CTCTTCAGTGAATGAAAAGAAGAGGAGGGAGCAGGAAGAAAGGCAGAATATTGTCCTGTAGAGACAGCCACTCATTACCT
TGCAGTATTTTTCTCTGGAAATCCTTGTAATCTTGAAGGAATGGACCTCAAAATTATGGCATCGTCAAAGCATTGTGGTG
TCTTTTTTACTGCTGCTTGCTGTGCTTATAGCTACGTATTATGTTGAAGGAGCGCATCAACAGTATGTGCAACGTATAGA
GAAACGGTTTCTTTTGAATGCCTACTGGATAGGCCTAGGAATTTTGTCTTCTGTTGGGCTTGGAACAGGGCTGCACACCT
TTCTGCTTTATCTGGGTCCACATATAGCCTCAGTTACATTAGCTGCTTATGAATGCAATTCAGTTAATTTTCCTGAACCA
CCCTATCCTGATTAGATTATTTGTCCAGATGAAGGGGGCACTGAAGGAACCATTTCTTTGTGGAGTATCATCTCAAAAGT
TAGGATTGAGGCCTGCATGTGGGGTATAGGTACAGCAATCGGAGAGCTGCCTCCGTATTTCATGGCCAGAGCAGCTCGCC
TCTCAGGTGCTGAACCAGATGATGAAGAGTATCAGGAATTTGAAAAGATGCTGGAACATGCAGAGTCTGCACAAGACTTT
GCCTCCCGGGCCAAACTGGCAGTTCAAAAACTAGTACAGAAAGTTGGATTTTTTGGAATTTTGGCCTGTGCTTCAATTCC
AAATCCTTTATTTGATCTGGCTGGAATAACATGTTGACACTTTCTGGTACCTTTTCGGACCGTCTTTGGTGCAACCCTAA
TTGGAAAAGCAATAATAAAAATGCATATCCAGAAAATTTTTGTTATAATAACATTCAGCAAGCACATAGTGGAGCAAATG
GTGGCTTTCATTGGTGCTGTCCCCGGCATAGGTCCATCTCTGCAGAAGCCATTTCAGGAGTACCTGGAGGCTCAACGGCA
GAAGCTTCACCACAAAAGCGAAATGGGCACACCACAGGGAGAAAACTGGTTGTCCTGGATGTTTGAAAAGTTGGTCGTTG
TCATGGTGTGTTACTTCATCCTGTCTATCATTAACTCCATGGCACAAAGTTATGCCAAACGCATCCAGCAGCGGTTGAAC
TCAGAGGAGAAAACTAAA

Alignment

ORF - retro_nleu_818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAENGKNCDQRRVAMNKEQHNGNFTDPSSVNEKKRREREERQNIVLWRQPLITLQYFSLEILVILKEWTS
          MAENGKNCDQRRVAMNKEQHNGNFTD.SSVNEKKRRE.EERQNIVL.RQPLITLQYFSLEILVILKEWTS
Retrocopy MAENGKNCDQRRVAMNKEQHNGNFTDLSSVNEKKRREQEERQNIVL*RQPLITLQYFSLEILVILKEWTS

Parental  KLWHRQSIVVSFLLLLAVLIATYYVEGAHQQYVQRIEKQFLLYAYWIGLGILSSVGLGTGLHTFLLYLGP
          KLWHRQSIVVSFLLLLAVLIATYYVEGAHQQYVQRIEK.FLL.AYWIGLGILSSVGLGTGLHTFLLYLGP
Retrocopy KLWHRQSIVVSFLLLLAVLIATYYVEGAHQQYVQRIEKRFLLNAYWIGLGILSSVGLGTGLHTFLLYLGP

Parental  HIASVTLAAYECNSVNFPEPPYPDQIICPDEGGTEGTISLWSIISKVRIEACMWGIGTAIGELPPYFMAR
          HIASVTLAAYECNSVNFPEPPYPD.IICPDEGGTEGTISLWSIISKVRIEACMWGIGTAIGELPPYFMAR
Retrocopy HIASVTLAAYECNSVNFPEPPYPD*IICPDEGGTEGTISLWSIISKVRIEACMWGIGTAIGELPPYFMAR

Parental  AARLSGAEPDDEEYQEFEEMLEHAESAQDFASRAKLAVQKLVQKVGFFGILACASIPNPLFDLAGITCGH
          AARLSGAEPDDEEYQEFE.MLEHAESAQDFASRAKLAVQKLVQKVGFFGILACASIPNPLFDLAGITC.H
Retrocopy AARLSGAEPDDEEYQEFEKMLEHAESAQDFASRAKLAVQKLVQKVGFFGILACASIPNPLFDLAGITC*H

Parental  FLVPFWTFFGATLIGKAIIKMHIQKIFVIITFSKHIVEQMVAFIGAVPGIGPSLQKPFQEYLEAQRQKLH
          FLVPF.T.FGATLIGKAIIKMHIQKIFVIITFSKHIVEQMVAFIGAVPGIGPSLQKPFQEYLEAQRQKLH
Retrocopy FLVPFRTVFGATLIGKAIIKMHIQKIFVIITFSKHIVEQMVAFIGAVPGIGPSLQKPFQEYLEAQRQKLH

Parental  HKSEMGTPQGENWLSWMFEKLVVVMVCYFILSIINSMAQSYAKRIQQRLNSEEKTK
          HKSEMGTPQGENWLSWMFEKLVVVMVCYFILSIINSMAQSYAKRIQQRLNSEEKTK
Retrocopy HKSEMGTPQGENWLSWMFEKLVVVMVCYFILSIINSMAQSYAKRIQQRLNSEEKTK

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_818 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000014339	1 retrocopy	retro_mdom_2,
Mus musculus	ENSMUSG00000018171	1 retrocopy	retro_mmus_2640,
Nomascus leucogenys	ENSNLEG00000000724	1 retrocopy	retro_nleu_818 ,
Rattus norvegicus	ENSRNOG00000003967	1 retrocopy	retro_rnor_527,
Sarcophilus harrisii	ENSSHAG00000016264	1 retrocopy	retro_shar_52,
Drosophila melanogaster	FBgn0052675	1 retrocopy	retro_dmel_49,