RetrogeneDB ID: retro_mmul_565

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:183178198..183179332(-)
• Located in intron of: None

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_565
TACTATGAAACATCCTGGAAATCTTTTAAAGGGTCTTGCAGACCCGCATCCAGGAACAGAGCCCTTTGCTCTCCCCTCAG
AATGAATGGACACCAGAAATCAGATATTTATGCCCAAGAAAAGCAGGATTTTGTTCGGTACTTCTCCCAGATTGTTAGGG
TGCTGACTGAGGAAAGATGGGGCACCCAGAGACAGAAGATGCTATTGCCCAGCTCAAGGAGGTCCTGGAGTGCAATGCAT
TGGAGGCAAGTATCCCCCAGGTTTGACGGTGCTAGTAGCATTTGGGGGAACTGATGGAGCCAAGGAAACAGGATGCTGAT
AGTCTCCAACGGGCCCTGACTGTGGGCTGGTGTGTGGAACTGCTGCAAGCTTTCTTCCTGGTGGTAGATGACATCATGGA
TTCATCCTTCACCTGCCGGGGACAGATCTGCTGTCAGAAGCTGGGCATGGATTTAGATGCCGTCAATGATGCTATCCTTC
TGGAAGCATGTATCTACCACCTGCTGAAGATCTATTGCCAGGAGCAGCCCTATTACCTGAACCTGACAGAGCTCTTCCTG
CAGAGTTCCTATCAGACTGAGATTAGGCAGACCCTGGACCTCATCCCAGCTCCCCAGGGCAATGTGGATCTTGGCAGATT
CACTGAAAAGAGACACAAATCTATTGTCAAGTACAAGACAGCTTTCTACTCCTTCTACCTTCCTGTAGCTGCAGCCATGT
ACATGGCAGGAATTGATGGCAAGAAGGAGCACAGCAATGCCAAGAAGATCCTGCTGGGGATGGAAGAGTTCTTTCAGGTT
CAGGATGATTACCTTGACCTCTTTGGGGACCCCAGTGTGACGGGTGAAGTTGACAGTGACATCTAGTACCAAAAATGCGG
TTGGCTGGTGGTTCAGTGTCTGCAACAGGCCATTCCGGAACAATACCAGATCCTGAAGGAAAATTCAGGCAGAAGGAAGC
CGAGAAGATGGCCTGGGTGAAGGCACTATATGAGGAGCTGGATCTGCCAGCCGTTTTCTTGCAATATGAGGAAGACACTT
ACAGTCACATTATAGGACTCACTGAACAGTATGCAGTGACCCTGCCCCCAGCATCTTTCTGGGGCTTGTGCACAAAATCT
ACAAGCGGAAAAAA

Alignment

ORF - retro_mmul_565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 90.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YPVLAWHSARCWCQAWTEEPRALCSSLRMNGDQKSDVYAQEKQDFVQHFSQIVRVLTED-EMGHPETGDA
          Y....W.S....C.......RALCS.LRMNG.QKSD.YAQEKQDFV..FSQIVRVLTE...MGHPET.DA
Retrocopy YYETSWKSFKGSCRPASRN-RALCSPLRMNGHQKSDIYAQEKQDFVRYFSQIVRVLTEE<KMGHPETEDA

Parental  IARLKEVLEYNA-IGGKYHRGLTVVVAFR-ELVEPRKQDADSLQRAWTVGWCVELLQAFFLVTDDIMDSS
          IA.LKEVLE.NA.IGGKY..GLTV.VAF..EL.EPRKQDADSLQRA.TVGWCVELLQAFFLV.DDIMDSS
Retrocopy IAQLKEVLECNA<IGGKYPPGLTVLVAFG>ELMEPRKQDADSLQRALTVGWCVELLQAFFLVVDDIMDSS

Parental  LTRRGQICWYQKPGVGLDAINDAILLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLITAP
          .T.RGQIC..QK.G..LDA.NDAILLEACIY.LLK.YC.EQPYYLNL.ELFLQSSYQTEI.QTLDLI.AP
Retrocopy FTCRGQICC-QKLGMDLDAVNDAILLEACIYHLLKIYCQEQPYYLNLTELFLQSSYQTEIRQTLDLIPAP

Parental  QGNVDLGRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLF
          QGNVDLGRFTEKR.KSIVKYKTAFYSFYLP.AAAMYMAGIDG.KEH.NAKKILL.M.EFFQ.QDDYLDLF
Retrocopy QGNVDLGRFTEKRHKSIVKYKTAFYSFYLPVAAAMYMAGIDGKKEHSNAKKILLGMEEFFQVQDDYLDLF

Parental  GDPSVTGKVGTDIQDNKCSWLVVQCLQRATPEQYQILKENYG-QKEAEKVARVKALYEELDLQAVFLQYE
          GDPSVTG.V..DI...KC.WLVVQCLQ.A.PEQYQILKEN.G.QKEAEK.A.VKALYEELDL.AVFLQYE
Retrocopy GDPSVTGEVDSDI*YQKCGWLVVQCLQQAIPEQYQILKENSG<QKEAEKMAWVKALYEELDLPAVFLQYE

Parental  EDSYSHIMALIEQYAAPLPPA-IFLGLARKIYKRKK
          ED.YSHI..L.EQYA..LPPA.IFLGL..KIYKRKK
Retrocopy EDTYSHIIGLTEQYAVTLPPA<IFLGLVHKIYKRKK

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	0.04 RPM	92.31 RPM
SRP007412_testis	0.00 RPM	61.93 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_565 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_565 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_565 has 0 orthologous retrocopies within eutheria group .

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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,