RetrogeneDB ID: retro_ptro_1048

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:39944616..39945683(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDPS
• Ensembl ID: ENSPTRG00000001422
• Aliases: None
• Description: None

Sequence

>retro_ptro_1048
AAAGCCCTTTGCTCCTCCCTCAGAATGAATGGAGACCAGAGATCAGATGTTTATGTCCAAGAAAAGCAGGATTTCGTTCA
GTACTTCTCCCAGATCATTGGGGATGAGATGAGGCACCCATAGACAGGAGATGCTATCACCCAGCTGAAGGAGATCCTGT
AGTACAATGCCATTGGGGCAAGTATCACCGGGGTTTGACAGTGCTAGTAGCATTCTGGGAGCTGGTGGAGCCAAGGAAAC
AGGATGCTGAGAGTCTCCAGCGGGCCCTGACTGTGGGCTGGTGTGTGGAACTGCTGCAAGCTTTGTTCCTGGTGGCAAAT
GACATCACGGATTCATTGCTTACCGCTGGTAACAGATCTGCTGGTTTCAGAAGCCGGGCGTGGGTTTGGATGCCATCAGT
GATGCTATCCTTGTGGAGCATGTATCTACTGCCTGCTGAAGCTCTATTGCTGGGAGCAGCCCTATTGCCAGAACCTGATC
CAGCTCTTCCTGCAGAGTTTCTATCAGACTGAGATTGGGCAGACCCTGGACCTCATCACAGCCCCCCAGGGCAATGCGGA
TCTTGGCAGATTCACTGAAAAGAGGTACAAATCTACTGTCAAGTACAAGGCAGTTTCTACTTCTACATTCCTGTAGCTGC
AGCCATGTACATGGCAGGCATTGATGGCGAGAAGGAGCACGACAATGCCAAGAAGATCCTGCTGGAGATGGGAGAGGGAG
AGTTCTTTCAGATCAGGATGATTACCTTCACCTCTTTTGGGGACCCCAGTGTGACCAGCAAAGTTGGCACTGACATCCAG
GACAATAAATGCAGCTGGCTGCTGGTTCAGTGTCTGCAACGGGCCACTCCCGAACACTACCAGATCCTGAAGGAGAATTA
CAGGCAGAAGGAGGCCAAGAAGGTGGCCCAGGTGAAGGCAGTATATGAGGAGCTGGATCTGCCGGCCGTGTTCTTGCAAT
AATAGAAAGACAGTTACAGCCACATTATGGGTCTCATTGAACAGTACACAGCTCCCCTGTCCCCAGCCATCTTTCTAGGG
CTGACATGCAAAATCTACAAAAGTAAA

Alignment

ORF - retro_ptro_1048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.08 %
• Parental protein coverage: 85.92 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RALCSSLRMNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIG-GKYNRG
          .ALCSSLRMNGDQ.SDVY.QEKQDFVQ.FSQ.......DEM.HP..GDAI..LKE.L.YNAIG.GKY.RG
Retrocopy KALCSSLRMNGDQRSDVYVQEKQDFVQYFSQ----IIGDEMRHP*TGDAITQLKEIL*YNAIG<GKYHRG

Parental  LTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLT-RRGQICWYQKPGVGLDAIN
          LTV.VAF.ELVEPRKQDA.SLQRA.TVGWCVELLQA.FLVA.DI.DS.LT.R..QICW.QKPGVGLDAI.
Retrocopy LTVLVAFWELVEPRKQDAESLQRALTVGWCVELLQALFLVANDITDSLLT<RW*QICWFQKPGVGLDAIS

Parental  DANLLE-ACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKY
          DA.L.E.ACIY.LLKLYC.EQPY..NLI.LFLQS.YQTEIGQTLDL.TAPQGN.DL.RFTEKRYKS.VKY
Retrocopy DAILVE<ACIYCLLKLYCWEQPYCQNLIQLFLQSFYQTEIGQTLDLITAPQGNADLGRFTEKRYKSTVKY

Parental  KT-AFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGE--FFQI-QDDYLDLF-GDPSVTGKIGTDIQD
          K...FY.FY.P.AAAMYMAGIDGEKEH.NAKKILLEMGE..FFQI.QDDYL.LF.GDPSVT.K.GTDIQD
Retrocopy KA<SFY-FYIPVAAAMYMAGIDGEKEHDNAKKILLEMGEGEFFQI<QDDYLHLF>GDPSVTSKVGTDIQD

Parental  NKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAA
          NKCSWL.VQCLQRATPE.YQILKENY.QKEA.KVA.VKA.YEELDLPAVFLQ...DSYSHIM.LIEQY.A
Retrocopy NKCSWLLVQCLQRATPEHYQILKENYRQKEAKKVAQVKAVYEELDLPAVFLQ**KDSYSHIMGLIEQYTA

Parental  PLPPAVFLGLARKIYKRR
          PL.PA.FLGL..KIYK..
Retrocopy PLSPAIFLGLTCKIYKSK

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_prefrontal_cortex	0.43 RPM	63.97 RPM
SRP007412_cerebellum	0.11 RPM	58.00 RPM
SRP007412_heart	0.00 RPM	30.14 RPM
SRP007412_kidney	0.03 RPM	85.10 RPM
SRP007412_liver	0.03 RPM	177.75 RPM
SRP007412_testis	0.11 RPM	36.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1048 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1048 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1048 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1558
Gorilla gorilla	retro_ggor_1184
Pongo abelii	retro_pabe_1290

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
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,