RetrogeneDB ID: retro_ptro_2561

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:126892297..126892701(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX2
• Ensembl ID: ENSPTRG00000012674
• Aliases: None
• Description: None

Sequence

>retro_ptro_2561
TTGTATCTTCAGTGGTTTGATGAAGCTAAATCTGGGAGATCACTCATGCTAGGTATGGATCTCCTTACCCTTGGCCTCTG
CATCATATTTTGGCCTATCAGAAATGGTGAAAAGTCAAATGTAAGATGAAAGCTATCAGATGGGGTAAGAAAACTCTGGA
CCAGGTCTTAGAAGATATAGACCAGTGCTGTCAAGCTCTCTCTAAAAGTCTGGTAACACAACCATATTTTTTTAATAAGC
AGCTTCCTGAATTTGATACACTGGTATTTGCCCATTTGTACACCATTCTTACCACACGATTGATGAATGATAAACTTTCT
GAGGTGAAAAACTACAGCAACCTTCTTGCTCTCTGCAGAAGAATTGAAAGGCACTATTTTGACGATTGTGATGAAGGCAG
ATTG

Alignment

ORF - retro_ptro_2561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.83 %
• Parental protein coverage: 51.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LYLQWCDEATVG-EITHARYGSPYPWPLNHILAYQKQWEVKRKMKAIGWGKKTLDQVLEDVDQCCQALSQ
          LYLQW.DEA..G.EITHARYGSPYPWPL.HILAYQK...VK.KMKAI.WGKKTLDQVLED.DQCCQALS.
Retrocopy LYLQWFDEAKSG<EITHARYGSPYPWPLHHILAYQKW*KVKCKMKAIRWGKKTLDQVLEDIDQCCQALSK

Parental  RLGTQPYFFNKQPTELDALVFGHLYTILTTQLTNDELSEKVKNYSNLLAFCRRIEQHYFEDRGKGRL
          .L.TQPYFFNKQ..E.D.LVF.HLYTILTT.L.ND.LSE.VKNYSNLLA.CRRIE.HYF.D...GRL
Retrocopy SLVTQPYFFNKQLPEFDTLVFAHLYTILTTRLMNDKLSE-VKNYSNLLALCRRIERHYFDDCDEGRL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	19.63 RPM
SRP007412_cerebellum	0.00 RPM	13.16 RPM
SRP007412_heart	0.00 RPM	18.92 RPM
SRP007412_kidney	0.00 RPM	34.39 RPM
SRP007412_liver	0.00 RPM	11.72 RPM
SRP007412_testis	0.00 RPM	52.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2561 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2561 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3780
Macaca mulatta	retro_mmul_1643

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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,