RetrogeneDB ID: retro_mmul_1245

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:6640072..6640698(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPIC
• Ensembl ID: ENSMMUG00000020873
• Aliases: None
• Description: None

Sequence

>retro_mmul_1245
TACCTGGTTTTCATCAGTGATTGTCCCCATGTCCGAGGAGATTCCAACTGCTGTGGAGTGTTGCTTACAGAGGAATCTAT
TTATAATTGGAGAACTTTAATAAATAATGCTGCAGACTTCTATTTTGAAGGAACTATTCATTGATCTTTGTGGAACATAA
CCGAAAGCCAGGTGGTACAGTCTGCTGTTTTCCAGCAAGAGGGAGGACAAGGCAGGAAGATGCTCTGTTTGAATAACTTC
ACAAATCTCAGTATAATCCCAAGATGGCATCTGTGTTCAGTAAGTAGATAAAACCAAAGGCAGTTTCCAGTTTGTATCAA
AAAACGAAGAAAAATTTGCCAAACTTTGAGGAATAAGGGCAACGGGAAGGCCATGATCAGAAAATGGCCAGGACACGGAG
GAATTACAGAAAAACTCAGGAAATCAGCAAAATCTGGAGAAAGCTCATTTACCAGTGAGCTTCAGTGGGGCCATTCTCTG
AAGATCTCTCCATCTTGTTTCTCGGAGAAAGAGATCGTCTACTCACAGTATGTTCAACTGATCAAGAACATCACAGTTTA
AATAATTGGAATGCAGACTAAAATTATACATATGCCAGTTACCATGAGCTTAGTCACTGTGATTGC

Alignment

ORF - retro_mmul_1245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.06 %
• Parental protein coverage: 85.83 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YLALINHRPHVKGSSSCYGVLPTEEPVYNWRTVINSAADFYFEGNIHQSLENITENQLVQPTVLQQKGGK
          YL..I...PHV.G.S.C.GVL.TEE..YNWRT.IN.AADFYFEG.IH.SL.NITE.Q.VQ..V.QQ.GG.
Retrocopy YLVFISDCPHVRGDSNCCGVLLTEESIYNWRTLINNAADFYFEGTIH*SLWNITESQVVQSAVFQQEGGQ

Parental  GRKKL-RLFEYLHESLCNPEMAS-CIQWVDKTKGIFQFVSKNKEKLAELWGKRKGNRK-TMTYQKMARAL
          G..K...LFE.LH.S..NP.MAS.C.Q.VDKTKG.FQFVSKN.EK.A.L.G.R...R......Q......
Retrocopy G-RKM<ALFE*LHKSQYNPKMAS<CVQ*VDKTKGSFQFVSKNEEKFAKL*GIRATGRP*SENGQDTEELQ

Parental  RNYGRSGEITKIRRKLTYQFSEAILQR-LSPSYFLGKEIFYSQCVQ-PDQEYLSLNNWNANYNYTYANYH
          .N.G......K....L...FS.AIL.R..SPS.F..KEI.YSQ.VQ..DQE..SLNNWNA..NYTYA.YH
Retrocopy KNSGNQQNLEKAH--LPVSFSGAIL*R<ISPSCFSEKEIVYSQYVQ<TDQEHHSLNNWNAD*NYTYASYH

Parental  ELNHHDC
          EL.H.DC
Retrocopy ELSHCDC

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	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.36 RPM
SRP007412_testis	0.04 RPM	2.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1245 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1245 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1800
Pan troglodytes	retro_ptro_1206
Gorilla gorilla	retro_ggor_1324

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009904	2 retrocopies	retro_btau_1281, retro_btau_1837,
Callithrix jacchus	ENSCJAG00000001906	1 retrocopy	retro_cjac_3835,
Dasypus novemcinctus	ENSDNOG00000004496	1 retrocopy	retro_dnov_759,
Equus caballus	ENSECAG00000009614	1 retrocopy	retro_ecab_542,
Echinops telfairi	ENSETEG00000004217	6 retrocopies	retro_etel_1675, retro_etel_2007, retro_etel_2008, retro_etel_593, retro_etel_929, retro_etel_933,
Homo sapiens	ENSG00000166211	4 retrocopies	retro_hsap_1748, retro_hsap_1800, retro_hsap_3135, retro_hsap_864,
Gorilla gorilla	ENSGGOG00000024597	4 retrocopies	retro_ggor_1324, retro_ggor_1362, retro_ggor_2255, retro_ggor_703,
Loxodonta africana	ENSLAFG00000015661	1 retrocopy	retro_lafr_912,
Myotis lucifugus	ENSMLUG00000011052	1 retrocopy	retro_mluc_2169,
Macaca mulatta	ENSMMUG00000020873	1 retrocopy	retro_mmul_1245 ,
Nomascus leucogenys	ENSNLEG00000006232	1 retrocopy	retro_nleu_53,
Oryctolagus cuniculus	ENSOCUG00000008070	1 retrocopy	retro_ocun_161,
Otolemur garnettii	ENSOGAG00000015148	1 retrocopy	retro_ogar_1782,
Pongo abelii	ENSPPYG00000004873	4 retrocopies	retro_pabe_1444, retro_pabe_1445, retro_pabe_2819, retro_pabe_686,
Pan troglodytes	ENSPTRG00000005351	4 retrocopies	retro_ptro_1206, retro_ptro_1218, retro_ptro_3070, retro_ptro_598,
Rattus norvegicus	ENSRNOG00000005720	1 retrocopy	retro_rnor_1519,
Ictidomys tridecemlineatus	ENSSTOG00000015457	3 retrocopies	retro_itri_1785, retro_itri_235, retro_itri_29,
Tursiops truncatus	ENSTTRG00000017205	1 retrocopy	retro_ttru_1708,