RetrogeneDB ID: retro_mmul_1248

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:17892429..17892714(-)
• Located in intron of: ENSMMUG00000002942

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9635
• Ensembl ID: ENSMMUG00000013275
• Aliases: None
• Description: brain protein I3 [Source:RefSeq peptide;Acc:NP_001253563]

Sequence

>retro_mmul_1248
CCCCTGCTGCCCACCCCTTGCTGCTGCCCACCCTCCCCTTATGTCATCACAGGGATACCCACCCACCACCCCAGGGTCTA
CAACGGCCACAGCCGGACTATCACTTGGTACCCTGCCAATGCCATCGTCATCATGAGAGGCTGTCCCGTCTGCAGGGACA
GGGTGCTGGAGGACTGCTTCACTTTCCTGGGAATCTTCCTGGCCATCATCCTGTTCCCCTTTGGGTTCATCTGCTATTTT
GCCTTGAGGAAGTGAAGATGCCCCAACTGCGGAGCAGCCTTTGCT

Alignment

ORF - retro_mmul_1248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 73.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAAPPP---PPYPYLVTGIPTHHPRVYNIHSRTVTRYPANSIVVVGGCPVCRVGVLEDCFTFLGIFLAII
          P..P.P...PP.PY..TGIPTHHPRVYN.HSRT.T.YPAN.IV...GCPVCR..VLEDCFTFLGIFLAII
Retrocopy PLLPTPCCCPPSPYVITGIPTHHPRVYNGHSRTITWYPANAIVIMRGCPVCRDRVLEDCFTFLGIFLAII

Parental  LFPFGFICCFALRKRRCPNCGATFA
          LFPFGFIC.FALRK.RCPNCGA.FA
Retrocopy LFPFGFICYFALRK*RCPNCGAAFA

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	6.16 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	18.56 RPM
SRP007412_cerebellum	0.13 RPM	4.52 RPM
SRP007412_heart	0.06 RPM	20.61 RPM
SRP007412_kidney	0.12 RPM	15.14 RPM
SRP007412_liver	0.00 RPM	81.70 RPM
SRP007412_testis	0.30 RPM	46.78 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1248 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1248 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015227	1 retrocopy	retro_cjac_2527,
Homo sapiens	ENSG00000164713	3 retrocopies	retro_hsap_1095, retro_hsap_1811, retro_hsap_195,
Gorilla gorilla	ENSGGOG00000009646	1 retrocopy	retro_ggor_205,
Microcebus murinus	ENSMICG00000002888	1 retrocopy	retro_mmur_372,
Macaca mulatta	ENSMMUG00000013275	2 retrocopies	retro_mmul_1248 , retro_mmul_849,
Otolemur garnettii	ENSOGAG00000000638	1 retrocopy	retro_ogar_63,
Pongo abelii	ENSPPYG00000025815	3 retrocopies	retro_pabe_1484, retro_pabe_50, retro_pabe_910,
Pan troglodytes	ENSPTRG00000019436	1 retrocopy	retro_ptro_698,
Tursiops truncatus	ENSTTRG00000015705	2 retrocopies	retro_ttru_706, retro_ttru_91,