RetrogeneDB ID: retro_mmul_2214

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:27700807..27701170(-)
• Located in intron of: ENSMMUG00000009840

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000004326
• Aliases: None
• Description: None

Sequence

>retro_mmul_2214
CTGACAGCCACTCAGGAAGCAATCTTGCATGCGTCGGGAAATGGCACATCCAAGGACTACTGCATGCTTTATAACCCCCA
TTGGTCAGCTCTTTCAAATACCCTAGAAAATGCAACTTACATTAGTTTGATGAATCTGACTTCCACACCACTATGCAACC
TTTCTGATGTTCCTCTTGTTGGCGTAAATTAGAACAAAGCAGTTGTGGTGCAATGGGGAAGCTGACATTTTCTTGAAAAC
ACCGGAATTGAACAGAAAAGAGGTGCTGAAGCAATGTTAGTTGTCAATAACAGTGTCCTATTTCCTACCTCAGGTAACAG
ATCTGAATTTCCTGATGTGAAAATACTGATTGCATTTATAAGC

Alignment

ORF - retro_mmul_2214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.51 %
• Parental protein coverage: 85.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTAAQEAILHASGNGTTKDYCMLYNPYWTTLPSTLENATSVSLMDLTSTPLCNLSDVPSVGIK-SKAVVV
          .TA.QEAILHASGNGT.KDYCMLYNP.W..L..TLENAT..SLM.LTSTPLCNLSDVP.VG....KAVVV
Retrocopy LTATQEAILHASGNGTSKDYCMLYNPHWSALSNTLENATYISLMNLTSTPLCNLSDVPLVGVN*NKAVVV

Parental  PWGSCQFFEKARIAQKGGAEAMLVVNNSVLFPPSGNRSEFPDVKILIAFIS
          .WGS..F.E...I.QK.GAEAMLVVNNSVLFP.SGNRSEFPDVKILIAFIS
Retrocopy QWGS*HFLENTGIEQKRGAEAMLVVNNSVLFPTSGNRSEFPDVKILIAFIS

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	0.11 RPM	1.01 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	0.87 RPM
SRP007412_cerebellum	0.13 RPM	4.78 RPM
SRP007412_heart	0.06 RPM	1.83 RPM
SRP007412_kidney	0.12 RPM	3.76 RPM
SRP007412_liver	0.00 RPM	4.31 RPM
SRP007412_testis	0.11 RPM	1.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2214 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2214 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2214 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000004326	1 retrocopy	retro_mmul_2214 ,