RetrogeneDB ID: retro_mmul_1882

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:59598233..59598709(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL43
• Ensembl ID: ENSMMUG00000010679
• Aliases: None
• Description: mitochondrial ribosomal protein L43 [Source:HGNC Symbol;Acc:14517]

Sequence

>retro_mmul_1882
ATGACTGCGCGCGGGACTCCTAGCCGCTTCTTGGCCAGTGTTCTGCACAACTGACTGGGTCGCTACGTGCAGCAGCTGCA
GCGTCTGAGCTTCAGCGTCAGCCGCGACGGCGCCTAGTCTCGCGGCGCCAGGGAGTTCGGGGAGCGGGAGGTGATCGACT
TCGCCCGACGGAACCCAGGGGTCGTAATATATGTGAATTCGCATCCGTGCTGCGTGCCCAGAGTAGTGACCGAATACCTT
AACGGGGTATGCGCGAGGAGAGCATCCACTGCAAGTCGGTCGAGGAGATCTCGACGCTGGTGCAGAAGCTGGCCAACCAG
TCGGGTTTGGACGTGATCCGCATCCGCAAGCCCTTCCACACCGACAATCCTAGCATCCAAGGCCAGTGGCACCCCTTCAC
CAACAAGCCGACCACTTTCCGCGGGCTATGCCCCCGAGAGGTTCAGGATCCTGCCCCAGCCCAGGTGCAAGCACAG

Alignment

ORF - retro_mmul_1882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 60.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTARGTPSRFLASVLHNGLGRYVQQLQRLSFSVSRDGASSRGAREFVEREVIDFARRNPGVVIYVNSRPC
          MTARGTPSRFLASVLHN.LGRYVQQLQRLSFSVSRDGA.SRGAREF.EREVIDFARRNPGVVIYVNS.PC
Retrocopy MTARGTPSRFLASVLHN*LGRYVQQLQRLSFSVSRDGA*SRGAREFGEREVIDFARRNPGVVIYVNSHPC

Parental  CVPRVVAEYLNG-SVREESIHCKSVEEISTLVQKLANQSGLDVIRIRKPFHTDNPSIQGQWHPFTNKPTT
          CVPRVV.EYLNG...REESIHCKSVEEISTLVQKLANQSGLDVIRIRKPFHTDNPSIQGQWHPFTNKPTT
Retrocopy CVPRVVTEYLNG<GMREESIHCKSVEEISTLVQKLANQSGLDVIRIRKPFHTDNPSIQGQWHPFTNKPTT

Parental  FRELCPREVQDPAPAQDAAE
          FR.LCPREVQDPAPAQ..A.
Retrocopy FRGLCPREVQDPAPAQVQAQ

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	16.70 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	40.38 RPM
SRP007412_cerebellum	0.00 RPM	20.02 RPM
SRP007412_heart	0.00 RPM	16.37 RPM
SRP007412_kidney	0.12 RPM	23.47 RPM
SRP007412_liver	0.00 RPM	32.82 RPM
SRP007412_testis	0.08 RPM	155.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1882 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1882 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1882 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009742	1 retrocopy	retro_cfam_1720,
Erinaceus europaeus	ENSEEUG00000004807	1 retrocopy	retro_eeur_444,
Echinops telfairi	ENSETEG00000012498	1 retrocopy	retro_etel_2213,
Microcebus murinus	ENSMICG00000000014	1 retrocopy	retro_mmur_370,
Macaca mulatta	ENSMMUG00000010679	1 retrocopy	retro_mmul_1882 ,
Nomascus leucogenys	ENSNLEG00000014812	1 retrocopy	retro_nleu_17,