RetrogeneDB ID: retro_mmul_1643

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:162885571..162885974(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX2
• Ensembl ID: ENSMMUG00000010185
• Aliases: MTX2, metaxin-2
• Description: metaxin-2 [Source:RefSeq peptide;Acc:NP_001248051]

Sequence

>retro_mmul_1643
TTGTATCTTCAGTGGTTGGATGAACCTAAATCGGGGAGATCACTCATGCTAGGTATGGATCTCCTTACCCTTCGCCTCTT
CATCATATTTTGGCCTATCAGAAACAGTGAAAAGTCAAATGTAAGGTGAAAGCCATCAGATGGGGTAAGAAGACTTTGGA
GCAGGTCTTAGAAGATATAGACCAGTGCTGTCAAGCTCTCTCTCAAAGTCTGGGAACATAACCATGTTTTTAAATAAGCA
GCTTTGTGAATTTGATACATTGGTATTTGGCCATTTGTACACCATTCTTACCACACAATTGATGAATGATAAACTTTCTG
AAGTGAAAAACTGCAGCAAACTTCTTGCTCTCTGCAAAAGAAATGAAAGGCACTATTTTGACTATTGTGAAAAAGGCAGA
ATG

Alignment

ORF - retro_mmul_1643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.19 %
• Parental protein coverage: 51.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LYLQWCDEAT-VGEITHARYGSPYPWPLNHILAYQKQWEVKRKMKAIGWGKKTLDQVLEDVDQCCQALSQ
          LYLQW.DE....GEITHARYGSPYP.PL.HILAYQKQ..VK.K.KAI.WGKKTL.QVLED.DQCCQALSQ
Retrocopy LYLQWLDEPK<IGEITHARYGSPYPSPLHHILAYQKQ*KVKCKVKAIRWGKKTLEQVLEDIDQCCQALSQ

Parental  RLGTQP-YFFNKQPTELDALVFGHLYTILTTQLTNDELSEKVKNYSNLLAFCRRIEQHYFEDRGKGRL
          .LGT.P..F.NKQ..E.D.LVFGHLYTILTTQL.ND.LSE.VKN.S.LLA.C.R.E.HYF....KGR.
Retrocopy SLGT*P<MFLNKQLCEFDTLVFGHLYTILTTQLMNDKLSE-VKNCSKLLALCKRNERHYFDYCEKGRM

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	0.00 RPM	19.94 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	16.18 RPM
SRP007412_cerebellum	0.00 RPM	15.11 RPM
SRP007412_heart	0.00 RPM	13.07 RPM
SRP007412_kidney	0.00 RPM	19.60 RPM
SRP007412_liver	0.00 RPM	5.19 RPM
SRP007412_testis	0.11 RPM	53.00 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1643 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1643 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3780
Pan troglodytes	retro_ptro_2561

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 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 ,
Macaca mulatta	ENSMMUG00000021104	1 retrocopy	retro_mmul_489,
Nomascus leucogenys	ENSNLEG00000006020	1 retrocopy	retro_nleu_1117,
Pan troglodytes	ENSPTRG00000012674	1 retrocopy	retro_ptro_2561,
Sarcophilus harrisii	ENSSHAG00000016381	1 retrocopy	retro_shar_162,