RetrogeneDB ID: retro_mmul_2061

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:176196913..176197452(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2032
• Ensembl ID: ENSMMUG00000005689
• Aliases: None
• Description: peroxiredoxin-2 [Source:RefSeq peptide;Acc:NP_001248186]

Sequence

>retro_mmul_2061
ATGGCCTCCGGTCAGTCGCAGCTCGGAGAGCCAGCCCCTGACTTCAAGGCCACTGCCCTGGTGGATGGCGCCTTCCAGGA
GGTGAAGCTGTGGGCTACGAAGGGAAGTACGTCGTCCTCTTTTTGTACCCTCTGGACTTCACTTTTCTATGGCCCACAGA
GAACATCGCTTTCAGTGACCTTGCCGAGGATTTCCACAAGCTGGGCTGCGAAGTGCTGGGTGTCTCGGTGGACTGAGTTC
ACCCACCTGAGTTGGATCAACAGCCCCCAGAAGTAGGGAGCCCTGGGCCCCCACGCATCTCCCACCTGCTGACATGATGG
GAAGCTTGTCTGAGGATTACGGTGTGCTGAAAACCCATGAGGGTGTTCCTACCCTGCCTCTTCATCATCGATGGCAAGGG
TGACCTTTGCCAGATAACTGCTACTGATTTGCCTGTGGGGCGCTCCATGGATGAGGCTCTGCGGCGGGTCCAGGCCTTCC
AATATGTGATCGAACACGGGGAAGTTTGTCCCACTGGCTGGAAGCCTGGTGGCAACAGT

Alignment

ORF - retro_mmul_2061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.96 %
• Parental protein coverage: 91.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MASGNARIGKPAPDFKATAVVDGAFKEVKL-SDYKGKYVVLFFYPLDFTFVCPTEIIAFSNRAED-FRKL
          MASG....G.PAPDFKATA.VDGAF.EVKL...Y.GKYVVLF.YPLDFTF..PTE.IAFS..AED.F...
Retrocopy MASGQSQLGEPAPDFKATALVDGAFQEVKL<VGYEGKYVVLFLYPLDFTFLWPTENIAFSDLAED<FPQA

Parental  GCEVLG-VSVDSQFTHLAWINTPRKEGGLG-PLNIPLLADVTRRLSEDYGVLKTDE-GIAYRG-LFIIDG
          G....G.VS....FTHL.WIN.P.K.G.LG.P...P..AD....LSEDYGVLKT.E.G..Y...LFIIDG
Retrocopy GLRSAG<VSRWTEFTHLSWINSPQK*GALG>PTHLPP-ADMMGSLSEDYGVLKTHE<GCSYPA<LFIIDG

Parental  KGVLRQITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSDT
          KG.L.QIT..DLPVGRS.DEALR.VQAFQY..EHGEVCP.GWKPG...
Retrocopy KGDLCQITATDLPVGRSMDEALRRVQAFQYVIEHGEVCPTGWKPGGNS

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	0.22 RPM	83.37 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	172.54 RPM
SRP007412_cerebellum	0.71 RPM	75.68 RPM
SRP007412_heart	0.41 RPM	69.84 RPM
SRP007412_kidney	0.23 RPM	84.97 RPM
SRP007412_liver	0.28 RPM	76.71 RPM
SRP007412_testis	0.19 RPM	2.07 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2061 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2061 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012307	3 retrocopies	retro_amel_1188, retro_amel_1710, retro_amel_55,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004882	4 retrocopies	retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Dipodomys ordii	ENSDORG00000009005	1 retrocopy	retro_dord_176,
Felis catus	ENSFCAG00000000473	1 retrocopy	retro_fcat_1755,
Homo sapiens	ENSG00000167815	3 retrocopies	retro_hsap_1184, retro_hsap_3278, retro_hsap_3500,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061 ,
Macaca mulatta	ENSMMUG00000006221	1 retrocopy	retro_mmul_762,
Macaca mulatta	ENSMMUG00000008294	2 retrocopies	retro_mmul_1307, retro_mmul_1517,
Macaca mulatta	ENSMMUG00000021366	1 retrocopy	retro_mmul_2001,
Monodelphis domestica	ENSMODG00000006978	1 retrocopy	retro_mdom_1770,
Mustela putorius furo	ENSMPUG00000004591	2 retrocopies	retro_mputfur_28, retro_mputfur_660,
Mus musculus	ENSMUSG00000005161	2 retrocopies	retro_mmus_2403, retro_mmus_472,
Nomascus leucogenys	ENSNLEG00000012800	2 retrocopies	retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii	ENSOGAG00000024998	2 retrocopies	retro_ogar_1993, retro_ogar_244,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000010541	3 retrocopies	retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Rattus norvegicus	ENSRNOG00000003520	2 retrocopies	retro_rnor_2288, retro_rnor_497,
Sorex araneus	ENSSARG00000000146	1 retrocopy	retro_sara_96,
Sarcophilus harrisii	ENSSHAG00000015596	1 retrocopy	retro_shar_305,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,