RetrogeneDB ID: retro_nleu_1117

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:15886044..15886450(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX2
• Ensembl ID: ENSNLEG00000006020
• Aliases: None
• Description: None

Sequence

>retro_nleu_1117
TTGTATCTTCAGTGGTTTGATGAAGCTAAATTGGGGAGATCACTCATGCTAGGTATGGATCTCCTTACCCGTGGCCTCTG
CATCATATTTTGGCCTATCAGAAATAGTGAAAAGTCAAATGTAAGATGAAAGCTATCAGATGGGGTAAGAGTACCCTGAA
CCAGGTCTTAGAAGATATAGGCCAGTGCTGTCAAGCTCTCTCTCTCAAAGTCTGGGAACACAACCATATTTTTTTAATAA
GCAGCTTCCTGAATTTGATACACTGGTATTTGGCCATTTGTACACCATTCTTCCCACACAATTGATGAATGATAAACTTT
CTGAGATGAAAAACTACAGCAAGCTTCTTGCTCTCTGCAGAAGAATTGAAAGGCACTATCTTGACTATTGTGATAAAGGC
AGATTG

Alignment

ORF - retro_nleu_1117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.22 %
• Parental protein coverage: 51.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LYLQWCDEAT-VGEITHARYGSPYPWPLNHILAYQKQWEVKRKMKAIGWGKKTLDQVLEDVDQCCQALSQ
          LYLQW.DEA...GEITHARYGSPYPWPL.HILAYQK...VK.KMKAI.WGK.TL.QVLED..QCCQALS.
Retrocopy LYLQWFDEAK<IGEITHARYGSPYPWPLHHILAYQK**KVKCKMKAIRWGKSTLNQVLEDIGQCCQALSL

Parental  RL-GTQSYF-FNKQPTELDALVFGHLYTILTTQLTNDELSEKVKNYSNLLAFCRRIEQHYFEDRGKGRL
          ...G....F.FNKQ..E.D.LVFGHLYTIL.TQL.ND.LSE..KNYS.LLA.CRRIE.HY.....KGRL
Retrocopy KV>GNTTIF>FNKQLPEFDTLVFGHLYTILPTQLMNDKLSE-MKNYSKLLALCRRIERHYLDYCDKGRL

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_1117 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009655	1 retrocopy	retro_chof_2429,
Cavia porcellus	ENSCPOG00000011099	1 retrocopy	retro_cpor_218,
Dipodomys ordii	ENSDORG00000003848	2 retrocopies	retro_dord_159, retro_dord_192,
Homo sapiens	ENSG00000128654	1 retrocopy	retro_hsap_3780,
Macaca mulatta	ENSMMUG00000010185	1 retrocopy	retro_mmul_1643,
Nomascus leucogenys	ENSNLEG00000006020	1 retrocopy	retro_nleu_1117 ,
Pan troglodytes	ENSPTRG00000012674	1 retrocopy	retro_ptro_2561,
Sarcophilus harrisii	ENSSHAG00000016381	1 retrocopy	retro_shar_162,