RetrogeneDB ID: retro_mmul_698

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214729635:2194..2836(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9754
• Ensembl ID: ENSMMUG00000020549
• Aliases: None
• Description: Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:F7D2A2]

Sequence

>retro_mmul_698
ATGGAACCACTAGACCTGGATAAGTGTGTGGAGATAGCGCGGCTGTACAAGTACCTGCCAGAGAATGACATGAAGCGGCT
ATGTGACTATGTTTGTGACCTCCACTTAGACGAGTCAAATGTTCAGCCAGTATCAGCACAACTAACAGTGTGTGGAGTTA
TACATGGATAGTTTTATGACCTTTGTGAACTATTCAGAACTGAAGGTCAGGTTCCTGACACAAACTGCATATTTATGGGT
GATTTTCTAGACAGAGGTTACTGCAGTTTGGAGACTTTCACTTACCTTCTTGCATTAAAGGTTAAACGACCTGATCATAT
TACACTTTTGCAATGAAATCATGAGAGTAGACAGATAACACAGGTTTATGGATTTTATGATGAGTGCCAAGCCAAATATG
GAAATGCCTAGAGATACTGTACCAAAGTTTTTGACATGCTCACAGTAGCAACTTTAATAGATGAGCAGATTTTTTGTGTC
CGTGGTGGTTTATCTCCTGATTTCAAAACGCTGGATCAAATTCGAACCATCGCATGGAATCAGGAAATTCTTCATAAAGG
AGCATTTTGTGATCTGGTTTGGTCAGATCCTGAAGATATGGATACTTGGGCTATCAGTCCCCGAAGAGCGATGTTTTTCT
AT

Alignment

ORF - retro_mmul_698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.87 %
• Parental protein coverage: 70.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPLDLDKYVEIARLCKYLPENDLKRLCDYVCDLLLEESNVQPVSTPVTVCGDIHGQFYDLCELFRTGGQ
          M.PLDLDK.VEIARL.KYLPEND.KRLCDYVCDL.L.ESNVQPVS...TVCG.IHG.FYDLCELFRT.GQ
Retrocopy MEPLDLDKCVEIARLYKYLPENDMKRLCDYVCDLHLDESNVQPVSAQLTVCGVIHG*FYDLCELFRTEGQ

Parental  VPDTNYIFMGDFVDRGYYSLETFTYLLALKAKWPDRITLLRGNHESRQITQVYGFYDECQTKYGNANAWR
          VPDTN.IFMGDF.DRGY.SLETFTYLLALK.K.PD.ITLL..NHESRQITQVYGFYDECQ.KYG..NA.R
Retrocopy VPDTNCIFMGDFLDRGYCSLETFTYLLALKVKRPDHITLLQ*NHESRQITQVYGFYDECQAKYG--NA*R

Parental  YCTKVFDMLTVAALIDEQILCVHGGLSPDIKTLDQIRTIERNQEIPHKGAFCDLVWSDPEDVDTWAISPR
          YCTKVFDMLTVA.LIDEQI.CV.GGLSPD.KTLDQIRTI..NQEI.HKGAFCDLVWSDPED.DTWAISPR
Retrocopy YCTKVFDMLTVATLIDEQIFCVRGGLSPDFKTLDQIRTIAWNQEILHKGAFCDLVWSDPEDMDTWAISPR

Parental  GAGWLF
          .A....
Retrocopy RAMFFY

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	37.42 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	22.77 RPM
SRP007412_cerebellum	0.06 RPM	36.81 RPM
SRP007412_heart	0.06 RPM	18.20 RPM
SRP007412_kidney	0.00 RPM	32.63 RPM
SRP007412_liver	0.04 RPM	11.76 RPM
SRP007412_testis	0.08 RPM	51.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_698 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_698 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_698 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012357	3 retrocopies	retro_chof_1759, retro_chof_183, retro_chof_608,
Dasypus novemcinctus	ENSDNOG00000015319	1 retrocopy	retro_dnov_1700,
Erinaceus europaeus	ENSEEUG00000010197	1 retrocopy	retro_eeur_706,
Macaca mulatta	ENSMMUG00000020549	1 retrocopy	retro_mmul_698 ,
Rattus norvegicus	ENSRNOG00000015145	1 retrocopy	retro_rnor_2074,
Sarcophilus harrisii	ENSSHAG00000008282	1 retrocopy	retro_shar_146,
Sus scrofa	ENSSSCG00000005600	1 retrocopy	retro_sscr_243,