RetrogeneDB ID: retro_ptro_2940

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03160806.1:3149..4206(-)
• 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_2940
AATGGAAACCAGACATCAGATGTTTATGCCCAAGAAAAGCAGGATTTCGTTCAGCACTACTCCCAGATCGTTAGGGTGCT
GACTGAGGATGAGATGGGGCACCCAGAGACAGGAGATGCTACTGCCCGGCTCAAGGAGGTCCTGGAGTACAATGCCATTG
GAGGCAAGTATCACCGAGGTTTGATGGTGCTAGTAGCGTTCCGGGAGCTGGTGGAGCCGAGGAAACAGGATGCTGATAGT
CTCCAGTGGGCACTGACTGTGGGCTGGTATGCGGAACTGCTGCAAGCTTTCTTCCTGGTGGGCAGATGACATTATGGATT
CATCCCTTACCTGCCAGGGACAGATCTCCTGGTATCAGAAGCTGGGCATGGGTTTGGATGCCATCAATGATGCTATCCTT
CTGGAAGCATGTATCTACTGCCTGCCGAAGCTGTATTGCCGGGAGCAGCCCTATTACCTGAACCTGATGGAGCTCTTCCA
GCAGAATTCTTATCAGACTGAGATTGGGCAGACCCTCGACCTCATCACAACCCCCCAGGGCAATGTGGATCTTCGCAGAT
GCACCGGAAAAAGGCACAAATCTGTTGTCAAGTACAAGACAGCTTTCTACTCCTTCTACCTTCCTGTAGCTGCAGCCATG
TACATGTCAAGAATGGATGACAAGAAGGAGCACACCAGTGCCAAGAAGATCCTGCTGGAGATTCAAGAGTTCTTTCAGAT
TCAGGATGATTACCTTGACTTCTTTGGGGACCCCAGTGTGACTGGCAGAGTTGGCAATGACTTCCAGGACAACAAATGCA
GCTGGCTGGTGGTTCAGTGTCTGCTACAGGCCACTCCAGAACAGTACCAGATCCTGAAGGAGAATTACAGGCAGAAGGAG
GCCGAGAAGGTGGCCCGGGTGAAGGCACTATACGAGGAGCTGGATCTGCCAGCCGTGTTCTTGCAGTATGAGAAAGACAG
TTACAGCCACGTTATGGGTCTCATCGAATAGTACGCAGAGCCCCTGACCCCAGCCATCTTTCTGGGGCTTGTGCACAAAA
TCTACAAGTGGAAAAAG

Alignment

ORF - retro_ptro_2940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.0 %
• Parental protein coverage: 84.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFREL
          NG.Q.SDVYAQEKQDFVQH.SQIVRVLTEDEMGHPE.GDA.ARLKEVLEYNAIGGKY.RGL.V.VAFREL
Retrocopy NGNQTSDVYAQEKQDFVQHYSQIVRVLTEDEMGHPETGDATARLKEVLEYNAIGGKYHRGLMVLVAFREL

Parental  VEPRKQDADSLQRAWTVGWCVELLQAFFLV-ADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIY
          VEPRKQDADSLQ.A.TVGW..ELLQAFFLV.ADDIMDSSLT..GQI.WYQK.G.GLDAINDA.LLEACIY
Retrocopy VEPRKQDADSLQWALTVGWYAELLQAFFLV>ADDIMDSSLTCQGQISWYQKLGMGLDAINDAILLEACIY

Parental  RLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPI
          .L.KLYCREQPYYLNL.ELF.Q.SYQTEIGQTLDL.T.PQGNVDL.R.T.KR.KS.VKYKTAFYSFYLP.
Retrocopy CLPKLYCREQPYYLNLMELFQQNSYQTEIGQTLDLITTPQGNVDLRRCTGKRHKSVVKYKTAFYSFYLPV

Parental  AAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATP
          AAAMYM...D..KEH..AKKILLE..EFFQIQDDYLD.FGDPSVTG..G.D.QDNKCSWLVVQCL..ATP
Retrocopy AAAMYMSRMDDKKEHTSAKKILLEIQEFFQIQDDYLDFFGDPSVTGRVGNDFQDNKCSWLVVQCLLQATP

Parental  EQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK
          EQYQILKENY.QKEAEKVARVKALYEELDLPAVFLQYE.DSYSH.M.LIE.YA.PL.PA.FLGL..KIYK
Retrocopy EQYQILKENYRQKEAEKVARVKALYEELDLPAVFLQYEKDSYSHVMGLIE*YAEPLTPAIFLGLVHKIYK

Parental  RRK
          ..K
Retrocopy WKK

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	0.00 RPM	63.97 RPM
SRP007412_cerebellum	0.00 RPM	58.00 RPM
SRP007412_heart	0.00 RPM	30.14 RPM
SRP007412_kidney	0.00 RPM	85.10 RPM
SRP007412_liver	0.00 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_2940 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2940 has 0 orthologous retrocopies within eutheria group .

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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,