RetrogeneDB ID: retro_mmul_2152

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:59059328..59060405(+)
• Located in intron of: ENSMMUG00000003364

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDPS
• Ensembl ID: ENSMMUG00000023144
• Aliases: None
• Description: None

Sequence

>retro_mmul_2152
AGAGCCCTATGCTCCTCCCTCAGAATGAATGGAGACCAGAAATCACATGTTTATGCCCAATAAAAGCGGGATTTCTTTCA
GCACTTTTCCCAGATCTTTGGGGTGCTGACTGAGGATGAGATGGGGCACCCAGAGACAGGAGATGCTATTGTCCGGCTCA
AGGTGGTCCTGGAGTACAATACCATTGGAGACAAGTATCACCGGGGTTTGACAATGCTAGTAGTGTTCCTGGAGCTGATG
GAGCCAAGGACACAGGATGCTGATAGTCTCCAGCAGGCCCTGAATGTAGGCTGGTGTCTGGAACTGCTGCAAGCTTTCTT
CCTGGTGACAGATGACATCACGGATTCATCCCTCACCCGCTGGGGACAGATCTGCTGTTATCAGAAGCCGGATGTGGGGT
AGGATGCCATCAATTATGTTATCCTTCTGGAAGCATGTATCTACTACCTGCTGAAGCTCTATTGCTGAGAGCAGCCCTAT
TACCTGAACCTGATCAAGCTCTTCCTACAGATTTTCTATCAGACTGAGATTGGGCAGCCCTGGACCTCGTTGCAGCCCCC
TAGGACAATGTGGATTTTGGCAGATTCACTGAAAAGAGGTACAAATCTATTGTCAAGTACAAGACAGCTTTCTACTCCTA
CCTTCCTGTAGCTGCAGCCATGCACATGGCAGGAATTGATGGCGAGAAGGAGCATGCCAATGCTTAGTAGATCCTACTGG
AGATGGGAGAGTTTTTTCAAATTCAGGATGATTACCTTGACCTCTTTGGGGACCCCATTGTGACCGGCAAAGTTGGCACT
GACATCCAGGACAACAACCTGCTGGCTGGTGGTTCAGTGTCTGCAGTGGTCCACTCTGGAACAGTACCAGATCCTGAAAG
AAAATTACAGACAGAAGAAGGTCAAGAAGGTAGTCCGAGTGAACGCACTGTATGAGGAGTTGGATCTGCCGGCTGCGTTC
TTGCAGTGTGAGGAAAACGGTTACAGCCACATTATGGGTCTCATTGAACAGTACGCAGCGCCCCTGCTCCCAGCCATCTT
TCTGGGGCTTGCGCGCAAAATCTACAAGCAGAAAAAG

Alignment

ORF - retro_mmul_2152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.09 %
• Parental protein coverage: 86.16 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RALCSSLRMNGDQKSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPETGDAIARLKEVLEYNAIGGKYHRGL
          RALCSSLRMNGDQKS.VYAQ.K.DF.QHFSQI..VLTEDEMGHPETGDAI.RLK.VLEYN.IG.KYHRGL
Retrocopy RALCSSLRMNGDQKSHVYAQ*KRDFFQHFSQIFGVLTEDEMGHPETGDAIVRLKVVLEYNTIGDKYHRGL

Parental  TVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVTDDIMDSSLTRRGQICWYQKPGVGLDAINDA
          T..V.F.EL.EPR.QDADSLQ.A..VGWC.ELLQAFFLVTDDI.DSSLTR.GQIC.YQKP.VG.DAIN..
Retrocopy TMLVVFLELMEPRTQDADSLQQALNVGWCLELLQAFFLVTDDITDSSLTRWGQICCYQKPDVG*DAINYV

Parental  ILLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQ-TLDLITAPQGNVDLGRFTEKRYKSIVKYKT
          ILLEACIY.LLKLYC.EQPYYLNLI.LFLQ..YQTEIGQ..LDL..AP..NVD.GRFTEKRYKSIVKYKT
Retrocopy ILLEACIYYLLKLYC*EQPYYLNLIKLFLQIFYQTEIGQ<ALDLVAAP*DNVDFGRFTEKRYKSIVKYKT

Parental  AFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKVGTDIQDNK-CSWL
          AFYS.YLP.AAAM.MAGIDGEKEHANA..ILLEMGEFFQIQDDYLDLFGDP.VTGKVGTDIQDN..C.WL
Retrocopy AFYS-YLPVAAAMHMAGIDGEKEHANA**ILLEMGEFFQIQDDYLDLFGDPIVTGKVGTDIQDNN>C-WL

Parental  VVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLQAVFLQYEEDSYSHIMALIEQYAAPLPPAI
          VVQCLQ..T.EQYQILKENY.QK...KV.RV.ALYEELDL.A.FLQ.EE..YSHIM.LIEQYAAPL.PAI
Retrocopy VVQCLQWSTLEQYQILKENYRQKKVKKVVRVNALYEELDLPAAFLQCEENGYSHIMGLIEQYAAPLLPAI

Parental  FLGLARKIYKRKK
          FLGLARKIYK.KK
Retrocopy FLGLARKIYKQKK

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	19.50 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	39.19 RPM
SRP007412_cerebellum	0.00 RPM	14.98 RPM
SRP007412_heart	0.00 RPM	12.42 RPM
SRP007412_kidney	0.00 RPM	37.32 RPM
SRP007412_liver	0.00 RPM	92.31 RPM
SRP007412_testis	0.11 RPM	61.93 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2152 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2152 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1519
Pan troglodytes	retro_ptro_1028
Gorilla gorilla	retro_ggor_1162

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030749	2 retrocopies	retro_cfam_1822, retro_cfam_1888,
Callithrix jacchus	ENSCJAG00000008364	11 retrocopies	retro_cjac_1066, retro_cjac_1217, retro_cjac_1395, retro_cjac_157, retro_cjac_2011, retro_cjac_2081, retro_cjac_2161, retro_cjac_299, retro_cjac_4154, retro_cjac_44, retro_cjac_70,
Echinops telfairi	ENSETEG00000001154	6 retrocopies	retro_etel_1770, retro_etel_1818, retro_etel_2179, retro_etel_730, retro_etel_743, retro_etel_990,
Homo sapiens	ENSG00000160752	6 retrocopies	retro_hsap_1519, retro_hsap_1558, retro_hsap_1560, retro_hsap_3871, retro_hsap_3872, retro_hsap_502,
Microcebus murinus	ENSMICG00000007468	1 retrocopy	retro_mmur_1148,
Macaca mulatta	ENSMMUG00000023144	3 retrocopies	retro_mmul_1190, retro_mmul_2152 , retro_mmul_565,
Mus musculus	ENSMUSG00000059743	5 retrocopies	retro_mmus_1028, retro_mmus_1552, retro_mmus_2802, retro_mmus_3625, retro_mmus_590,
Nomascus leucogenys	ENSNLEG00000012099	6 retrocopies	retro_nleu_1486, retro_nleu_1727, retro_nleu_2301, retro_nleu_2405, retro_nleu_2595, retro_nleu_2692,
Pongo abelii	ENSPPYG00000000747	3 retrocopies	retro_pabe_1290, retro_pabe_1329, retro_pabe_235,
Pan troglodytes	ENSPTRG00000001422	9 retrocopies	retro_ptro_1028, retro_ptro_1048, retro_ptro_1049, retro_ptro_2637, retro_ptro_2638, retro_ptro_2639, retro_ptro_2940, retro_ptro_2995, retro_ptro_377,
Rattus norvegicus	ENSRNOG00000043377	3 retrocopies	retro_rnor_1175, retro_rnor_153, retro_rnor_2897,
Ictidomys tridecemlineatus	ENSSTOG00000004475	1 retrocopy	retro_itri_488,
Tursiops truncatus	ENSTTRG00000013326	1 retrocopy	retro_ttru_689,