RetrogeneDB ID: retro_mmul_1731

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:148783296..148783944(-)
• Located in intron of: ENSMMUG00000015535

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL24
• Ensembl ID: ENSMMUG00000000039
• Aliases: None
• Description: mitochondrial ribosomal protein L24 [Source:RefSeq peptide;Acc:NP_001244773]

Sequence

>retro_mmul_1731
ATGCGTCTTTCTGCCCTACTGGCCTTGGCATCCAAGGTCACTCTGCCCCCCAATTACTGCTATGGGATGAGCCCCTCAGG
CTCCTTGGCAGACAAGAGGAAGAACGCCCCATGGAGCAGGCGGCGCCCAGTGGTTGTGGAACCCATCTCTGATGAAGACT
GGTATCTGTTCTGTGGGGACACGGTGGAGATCCTAGAAGGCAAGGATGCCGGAAAGCAGGGCAAAGTGGTTCAAGTTATC
CGGCAGCAAAACTGCGTGGTCGTGGGAGGGCTGAACACATATTACCGCTACATTGGCAAGACCATGGATTACCGAGGAAC
CATGATCCCTAGTGAAGCCCCCTTGCTCCACCGCCAGGTCAAACTTGTGGATCCTATGGACAGGAAACCCACTGAGATTG
AGTGGAGATTTACTGAAGCAGGAGAGCGGGTACGAGTCTCCACACGATCGGGGAGAATTATCCCTAAACCCGAATTTCCC
AGAGCTGATGGCATCGTCCCTGAAACATGGATTGATGGCCCCAAAGACACATCAGTGGAAGATGCTTTAGAAAGAACCTA
CGTGCCCCGTCTAAAGACACTACAGGAGGAGGTGATGGAGGCCATGGGGATCAAGGAGACTCGGAAATACAAGAAGGTCT
ATTGGTAT

Alignment

ORF - retro_mmul_1731 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRLSALLALASKVTLPPNYCYGMSPSGSLADKRKNAPWSRRRPVVVEPISDEDWYLFCGDTVEILEGKDA
          MRLSALLALASKVTLPPNYCYGMSPSGSLADKRKNAPWSRRRPVVVEPISDEDWYLFCGDTVEILEGKDA
Retrocopy MRLSALLALASKVTLPPNYCYGMSPSGSLADKRKNAPWSRRRPVVVEPISDEDWYLFCGDTVEILEGKDA

Parental  GKQGKVVQVIRQQNCVVVGGLNTYYRYIGKTVDYRGTMIPSEAPLLHRQVKLVDPMDRKPTEIEWRFTEA
          GKQGKVVQVIRQQNCVVVGGLNTYYRYIGKT.DYRGTMIPSEAPLLHRQVKLVDPMDRKPTEIEWRFTEA
Retrocopy GKQGKVVQVIRQQNCVVVGGLNTYYRYIGKTMDYRGTMIPSEAPLLHRQVKLVDPMDRKPTEIEWRFTEA

Parental  GERVRVSTRSGRIIPKPEFPRADGIVPETWIDGPKDTSVEDALERTYVPRLKTLQEEVMEAMGIKETRKY
          GERVRVSTRSGRIIPKPEFPRADGIVPETWIDGPKDTSVEDALERTYVPRLKTLQEEVMEAMGIKETRKY
Retrocopy GERVRVSTRSGRIIPKPEFPRADGIVPETWIDGPKDTSVEDALERTYVPRLKTLQEEVMEAMGIKETRKY

Parental  KKVYWY
          KKVYWY
Retrocopy KKVYWY

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	6.95 RPM
SRP007412_brain_prefrontal_cortex	1.43 RPM	23.16 RPM
SRP007412_cerebellum	0.06 RPM	5.94 RPM
SRP007412_heart	0.24 RPM	20.43 RPM
SRP007412_kidney	0.12 RPM	12.09 RPM
SRP007412_liver	0.36 RPM	31.79 RPM
SRP007412_testis	0.49 RPM	15.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1731 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1731 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1731 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011340	1 retrocopy	retro_ecab_495,
Macaca mulatta	ENSMMUG00000000039	1 retrocopy	retro_mmul_1731 ,
Otolemur garnettii	ENSOGAG00000016825	1 retrocopy	retro_ogar_1541,