RetrogeneDB ID: retro_pabe_235

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:38339499..38340577(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDPS
• Ensembl ID: ENSPPYG00000000747
• Aliases: None
• Description: farnesyl pyrophosphate synthase [Source:RefSeq peptide;Acc:NP_001125620]

Sequence

>retro_pabe_235
AGAGCCCTTTGCTCCTCCCTCAGAATGAATAGAGACCAAAAATCAGATGCTTACGCCCAAGAAAAACAGGATTTCATTCA
GCACTTCTCCCGGATTGTTAGGGTGCTGACTGAGAATGAGATGGGGCACCCAGAGACAGGAGATGCTATCACCCGGCTCA
AGGAGGTCCTGGAGTATAATGCCATCGGAGGCAAGTTATCACCGGGGTTTGATGGTGCTTAGCATTCCAGGAGCTGGTGG
AGCCGAGGAAACAGGATGCTGATAGTTTCCAGCGGACCCTGACTGTGGGTTGGTGTGTGGAACTGCTGCAAACTTTCTTC
CTGGTGGCAGATGACATCACGGATTCATCCTTCACCCACTGGGGACAGATCTGCTGGTATCAGAAGCCGGGCGTGGGTTT
GGATGCTGTCAATGATGCTATGCTTCTGGAAGCATGTATCTACTGCCTGCTAAAGCTCTATTGCTGGGAGCAGCCCTATT
ACCTGAACCTGATCAAGCTCTTCCTGCAGAGTTCCTATCAGACCGAGATTGGGCAGACCCTGGACCTCATCACAGCCCCC
CAGGGCAATGTGGATCTTGGCAGATTCACTGAAAAGAGGTACAAATCTATTGCCAAGTGCAAGGCAGCTTTCTACTCCTA
CCTTCCTGTAGCTGCAGCCATGTACGTGGCAGGAATTGATGGCGAGAAGGAGCACGCTAATAGCAAGAAGATCCTGCTGG
AGATGGGAGAGTTCTTTCAGATTCAGGATGATTACCTTGACCTCTTTGGGGACCCCAGTGTGACCAGCAAAGTTGGCACT
GACATCCAGGACAACAAATGCGGTTGGCTGGTGGTTCAGTGTCTGCAACAGGCCACTCCAGAATAGTACCAGATCCTGAA
GGAGAACTACCGGCAGAAGGAGGCCAAGAAGGTGGCCCAGGTGAAGGCACTATATGAGGAGCTGGATCTGCCGGCTGTGT
TCTTGCAATATGAGGAAGACAGTTACAGCCACATTATGGGTCTCATTGAACAGTACGCAGCACCCCGACCCCAGCCATCT
TTCTGGGGCTGGTGCTCAAAATCTATAAGCAGAAAAAA

Alignment

ORF - retro_pabe_235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.57 %
• Parental protein coverage: 82.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RALCSSLRMNGDQKSDVYAQEKQDFVQHFSQIVRMLTEDEMGHPETGDAIARLKEVLEYNAIGGKYHRGL
          RALCSSLRMN.DQKSD.YAQEKQDF.QHFS.IVR.LTE.EMGHPETGDAI.RLKEVLEYNAIGGK...G.
Retrocopy RALCSSLRMNRDQKSDAYAQEKQDFIQHFSRIVRVLTENEMGHPETGDAITRLKEVLEYNAIGGKLSPGF

Parental  TVV-VAFRELVQPRKQDADSLQRARTVGWCVELV--FFLVADDIMDSSLTRRGQICWYQKPGVGLDAIND
          .....AF.ELV.PRKQDADS.QR..TVGWCVEL...FFLVADDI.DSS.T..GQICWYQKPGVGLDA.ND
Retrocopy DGA<LAFQELVEPRKQDADSFQRTLTVGWCVELLQTFFLVADDITDSSFTHWGQICWYQKPGVGLDAVND

Parental  ANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLITAPQGNVDLVRFTEKRYKSIVKYKT
          A.LLEACIY.LLKLYC.EQPYYLNLI.LFLQSSYQTEIGQTLDLITAPQGNVDL.RFTEKRYKSI.K.K.
Retrocopy AMLLEACIYCLLKLYCWEQPYYLNLIKLFLQSSYQTEIGQTLDLITAPQGNVDLGRFTEKRYKSIAKCKA

Parental  AFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLV
          AFYS.YLP.AAAMY.AGIDGEKEHAN.KKILLEMGEFFQIQDDYLDLFGDPSVT.K.GTDIQDNKC.WLV
Retrocopy AFYS-YLPVAAAMYVAGIDGEKEHANSKKILLEMGEFFQIQDDYLDLFGDPSVTSKVGTDIQDNKCGWLV

Parental  VQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLP-PAI
          VQCLQ.ATPE.YQILKENY.QKEA.KVA.VKALYEELDLPAVFLQYEEDSYSHIM.LIEQYAAP.P.PAI
Retrocopy VQCLQQATPE*YQILKENYRQKEAKKVAQVKALYEELDLPAVFLQYEEDSYSHIMGLIEQYAAPRP<PAI

Parental  FLGLARKIYKRRK
          FLGL..KIYK..K
Retrocopy FLGLVLKIYKQKK

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	0.06 RPM	44.23 RPM
SRP007412_cerebellum	0.00 RPM	34.53 RPM
SRP007412_heart	0.00 RPM	10.08 RPM
SRP007412_kidney	0.00 RPM	36.16 RPM
SRP007412_liver	0.00 RPM	75.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_235 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_235 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_502
Pan troglodytes	retro_ptro_377

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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,