RetrogeneDB ID: retro_mmul_1578

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:28899545..28899955(-)
• Located in intron of: ENSMMUG00000020274

Retrocopy information

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

Parental gene information

• Parental gene symbol: C20orf27
• Ensembl ID: ENSMMUG00000022079
• Aliases: None
• Description: chromosome 20 open reading frame 27 [Source:HGNC Symbol;Acc:15873]

Sequence

>retro_mmul_1578
ATGATCATGGTCACCCAGGACAGCGACAGCAGCTTTCTGGTCAAGGTTGGCCTCCTGAAGATCCTGCGCAGATATGAGAT
TACCTTCACTCTGCCCCCGCCCAGTGCGCAGGCTGAGCAAGGACATCCGCGAGGCACCTGTCCCCAACCTCTGCATGTCA
AGCTCCTCAGCGTCGTACCTGTCCCTGAAGGTTACAGTGTCAAGTGTGAATACTTGGCGCACAGAGAGGGCATCCTCAAA
GCAGAGATGCTGCCAGCCCGCGAAGGTGGCGCCGGCGCCTCTGTGCGCATGGTGGTGCAGGCAGGCGCCAGAGGCGGACA
CCACTGCGTGCCCACCTGCGGGATGGTGTCAAGGGCTCGCGCGCAACACTGGAATAAGACTTGCAGCACAGCCACTGGAA
CGGCTTTGAC

Alignment

ORF - retro_mmul_1578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.59 %
• Parental protein coverage: 77.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVMVTQESDSSFLVKVGFLKILHRYEITFTL-PPVHRLSKDVREAPVPS-LHLKLLSVVPVPEGYSVKCE
          ..MVTQ.SDSSFLVKVG.LKIL.RYEITFTL.PP.............P..LH.KLLSVVPVPEGYSVKCE
Retrocopy MIMVTQDSDSSFLVKVGLLKILRRYEITFTLPPPSAQAEQGHPRGTCPQPLHVKLLSVVPVPEGYSVKCE

Parental  YSAHKEGVLKEEILLACEGGTGTCVRVTVQARVMDRHHGTPM-LLDGVKCVGAELEYDSEHSDWHGFD
          Y.AH.EG.LK.E.L.A.EGG.G..VR..VQA.....HH..P..L.DGVK...A.LE.D..HS.W.GFD
Retrocopy YLAHREGILKAEMLPAREGGAGASVRMVVQAGARGGHHCVPT<LRDGVKGSRATLE*DLQHSHWNGFD

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	5.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	29.59 RPM
SRP007412_cerebellum	0.00 RPM	5.10 RPM
SRP007412_heart	0.00 RPM	3.06 RPM
SRP007412_kidney	0.00 RPM	2.93 RPM
SRP007412_liver	0.16 RPM	19.79 RPM
SRP007412_testis	1.51 RPM	56.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1578 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1578 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021194	1 retrocopy	retro_cjac_3292,
Homo sapiens	ENSG00000101220	2 retrocopies	retro_hsap_1114, retro_hsap_1673,
Gorilla gorilla	ENSGGOG00000016987	1 retrocopy	retro_ggor_871,
Macaca mulatta	ENSMMUG00000022079	1 retrocopy	retro_mmul_1578 ,
Nomascus leucogenys	ENSNLEG00000007653	1 retrocopy	retro_nleu_194,
Pongo abelii	ENSPPYG00000010813	1 retrocopy	retro_pabe_923,
Pan troglodytes	ENSPTRG00000013204	2 retrocopies	retro_ptro_1136, retro_ptro_685,