RetrogeneDB ID: retro_mmul_61

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:33530764..33531304(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000015343
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.625
• Ensembl ID: ENSMMUG00000017037
• Aliases: None
• Description: mitochondrial ribosomal protein L18 [Source:RefSeq peptide;Acc:NP_001252787]

Sequence

>retro_mmul_61
AAGGCGCTTCGCTCGCGGTTCTGGGGGTTCTCCGTTTGCAGGAACCCTGGGTGCAGGTTCGCAGCCCTCTCAACCAGCTC
CAAGCCGGCGGCGAAACCTGAAGTGCACCCTGTGGAAAATGAAGCTGTCACCCCAGAGTTCACCAATCGGAACCCCCGGA
ACCTGGAGCTTCTATCTGTAGCCAGGAAAGAGCGGGGCTGGCTGACGGTGTGGCCCTCCCGTGAGTTCTGGCACAGGTTG
CGAGTTATAAGGACTCAGCGTCATGTAGAAGCACTTGTGGAGCATCAAAATGGCAAAGTTGTGGTTTCGGCATCCACTCG
TGAATGGGCTATTAAAAAGCACCTTTATAGTACCAGAAATGTGGTGGCTTGTGAGAGTATAGGACGAGTACTGGCACAGA
GATGCTTAGAGGCGGGAATCAACTTCATGGTCTACCAACCAACCCCATGGGAGGCAGCCTTAGACTCGATGAAACGACTA
CAAAGTGCCATGACAGAAGGTGGTTTGGTTCTACGGGAACCTCAGAGAATCTATGAATAA

Alignment

ORF - retro_mmul_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.75 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALRSRFWGFSVCRNPGCRFAALSTSSKPAAKPEVHPVENEAVAPEFTNRNPRNLELLSVARKERGWRTVW
          ALRSRFWGFSVCRNPGCRFAALSTSSKPAAKPEVHPVENEAV.PEFTNRNPRNLELLSVARKERGW.TVW
Retrocopy ALRSRFWGFSVCRNPGCRFAALSTSSKPAAKPEVHPVENEAVTPEFTNRNPRNLELLSVARKERGWLTVW

Parental  PSREFWHRLRVIRTQRHVEALVEHQNGKVVVSASTREWAIKKHLYSTRNVVACESIGRVLAQRCLEAGIN
          PSREFWHRLRVIRTQRHVEALVEHQNGKVVVSASTREWAIKKHLYSTRNVVACESIGRVLAQRCLEAGIN
Retrocopy PSREFWHRLRVIRTQRHVEALVEHQNGKVVVSASTREWAIKKHLYSTRNVVACESIGRVLAQRCLEAGIN

Parental  FMVYQPTPWEAASDSMKRLQSAMTEGGVVLREPQRIYE
          FMVYQPTPWEAA.DSMKRLQSAMTEGG.VLREPQRIYE
Retrocopy FMVYQPTPWEAALDSMKRLQSAMTEGGLVLREPQRIYE

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	5.94 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	20.94 RPM
SRP007412_cerebellum	0.00 RPM	8.91 RPM
SRP007412_heart	0.00 RPM	11.54 RPM
SRP007412_kidney	0.00 RPM	8.92 RPM
SRP007412_liver	0.00 RPM	9.22 RPM
SRP007412_testis	0.04 RPM	17.38 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_61 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_61 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_61 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015398	1 retrocopy	retro_amel_1445,
Dipodomys ordii	ENSDORG00000011514	1 retrocopy	retro_dord_741,
Echinops telfairi	ENSETEG00000007591	1 retrocopy	retro_etel_438,
Homo sapiens	ENSG00000112110	1 retrocopy	retro_hsap_1664,
Gorilla gorilla	ENSGGOG00000014075	1 retrocopy	retro_ggor_1255,
Macaca mulatta	ENSMMUG00000017037	1 retrocopy	retro_mmul_61 ,
Mus musculus	ENSMUSG00000057388	1 retrocopy	retro_mmus_1940,
Otolemur garnettii	ENSOGAG00000007327	1 retrocopy	retro_ogar_1660,
Pongo abelii	ENSPPYG00000017147	3 retrocopies	retro_pabe_1416, retro_pabe_1418, retro_pabe_1421,
Pan troglodytes	ENSPTRG00000018761	1 retrocopy	retro_ptro_1128,
Pteropus vampyrus	ENSPVAG00000005322	2 retrocopies	retro_pvam_1480, retro_pvam_252,
Tarsius syrichta	ENSTSYG00000005598	1 retrocopy	retro_tsyr_1847,