RetrogeneDB ID: retro_mmul_2351

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:75778712..75779162(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10197
• Ensembl ID: ENSMMUG00000021773
• Aliases: None
• Description: None

Sequence

>retro_mmul_2351
AATAGAGCTATGATTATGGCTGGGCGGAGGCCGGGCTGTTTCCTCTGTTGAGAGGAAGCTGCGGATCTGTCCTCCCTGAA
ACCCATGTTGGACGAGCTGGGAGTCCCCCTCTTTGCAGGGGTAAAGGAGCACATCAGGACTGAAGTGAAGGATTTCCAGC
CTTATTTCAAAGGAGAAATCTTCCTGGATGAAAAGAAAAAGTTCTATGGTCCACAAAGGCGGAAGATGATGTTTTTGGGA
TTTCTCCATCTGGGAGTGTGGTACTTCTTCTGAGCCTGGAATGGAGGCTTCTCTGGAAACCTGGAAGGAGAAGGCTTCAT
CCTCAGGGACGTTTTCGTGGTAGGATCAGGAAACGAGGGGATTCTTCTCGAGCACTGAGAAAAATAATTTGGAGACAAAG
TAAATCTGCTTTGTCTGGTTCGGGAAGCTGCTGAGATGATCAAACCACAG

Alignment

ORF - retro_mmul_2351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.11 %
• Parental protein coverage: 67.57 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGAVIMAVRRPGCFLCREEAADLSSLKSMLDQLGVPLYAVVKEHIRTEVEDFQPYFKGEIFLDEKKKFYG
          N.A.IMA.RRPGCFLC.EEAADLSSLK.MLD.LGVPL.A.VKEHIRTEV.DFQPYFKGEIFLDEKKKFYG
Retrocopy NRAMIMAGRRPGCFLC*EEAADLSSLKPMLDELGVPLFAGVKEHIRTEVKDFQPYFKGEIFLDEKKKFYG

Parental  PQRRKMMFMGFIRLGVWYNFFRAWNGGFSGNLEGEGFILGGVFVVGSGKQGILLEHREKEFGDKVNLLS-
          PQRRKMMF.GF..LGVWY.FF.AWNGGFSGNLEGEGFIL..VFVVGSG..GILLEH.EK.FGDKVNLL..
Retrocopy PQRRKMMFLGFLHLGVWY-FF*AWNGGFSGNLEGEGFILRDVFVVGSGNEGILLEH*EK*FGDKVNLLCL

Parental  VLEAAKMIKPQ
          V.EAA.MIKPQ
Retrocopy VREAAEMIKPQ

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	4.93 RPM	52.55 RPM
SRP007412_brain_prefrontal_cortex	3.97 RPM	48.87 RPM
SRP007412_cerebellum	1.29 RPM	10.40 RPM
SRP007412_heart	1.06 RPM	29.03 RPM
SRP007412_kidney	2.46 RPM	41.90 RPM
SRP007412_liver	1.54 RPM	19.16 RPM
SRP007412_testis	1.58 RPM	24.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2351 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2351 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2351 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4076
Pan troglodytes	retro_ptro_2763
Gorilla gorilla	retro_ggor_2733
Pongo abelii	retro_pabe_3345

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000813	1 retrocopy	retro_chof_878,
Callithrix jacchus	ENSCJAG00000003657	1 retrocopy	retro_cjac_3312,
Dasypus novemcinctus	ENSDNOG00000001981	3 retrocopies	retro_dnov_1843, retro_dnov_1901, retro_dnov_868,
Homo sapiens	ENSG00000122378	2 retrocopies	retro_hsap_1135, retro_hsap_4076,
Gorilla gorilla	ENSGGOG00000013246	2 retrocopies	retro_ggor_2733, retro_ggor_886,
Microcebus murinus	ENSMICG00000007485	2 retrocopies	retro_mmur_1346, retro_mmur_1481,
Macaca mulatta	ENSMMUG00000021773	3 retrocopies	retro_mmul_2351 , retro_mmul_2409, retro_mmul_881,
Mus musculus	ENSMUSG00000021792	1 retrocopy	retro_mmus_2227,
Otolemur garnettii	ENSOGAG00000013638	7 retrocopies	retro_ogar_2126, retro_ogar_2435, retro_ogar_2562, retro_ogar_3327, retro_ogar_420, retro_ogar_580, retro_ogar_784,
Procavia capensis	ENSPCAG00000009696	1 retrocopy	retro_pcap_281,
Pongo abelii	ENSPPYG00000025862	4 retrocopies	retro_pabe_3345, retro_pabe_643, retro_pabe_738, retro_pabe_944,
Pan troglodytes	ENSPTRG00000002685	2 retrocopies	retro_ptro_2763, retro_ptro_774,
Rattus norvegicus	ENSRNOG00000011140	1 retrocopy	retro_rnor_1517,