RetrogeneDB ID: retro_nleu_2595

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397378.1:4074483..4075578(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDPS
• Ensembl ID: ENSNLEG00000012099
• Aliases: None
• Description: None

Sequence

>retro_nleu_2595
ACATCCAGGAACAGAGCCCTTTGCTCCTCCCTCAGAATGAATGGAGACCAGAAATCAGATGTTTATGCCCAAGAAAAGCA
GGATTTCTTTCAGCACTTCTCCCAGATCGTTGGGGTGCTGACTGAGGATGAGATGGGGCACTCAGAGACAGGAGATGCTA
TTGCCCGGCTCAAGGAGGTCCTGGAGTACAATGCCATTGGAGGCAAGTATCACCGGGGTTTGACGGTGCTAGTAGTGTTC
CAGGAGCTGGTGGAGCCAAGGAAACAGGATGCTGATAGTCTCCAGAGGGCCCTGACTGTGGGCTGGTGTGTGGAACTGCT
GCAAGCTTTCTTCCTGGTGACAGATGACATCATGGATTCATCCCTCACCCGCTGGGGACAGATCTGCTGTTATCAGAAGA
TGGGTATGGGGTAGGATGCCATCAATTATGGTATCCTTCTGCAAGCATGTATCTACTACCTGCTGAAGCTCTACTGCCGA
GAGCAGCCCTATTACCTGAACCTGATCGAGCTCTTCCTGCAGATTTCCTATCAGCCTGAGATTGGGCAGACCCTGGACCT
CACCACAGCCCCCTAGGACAATGTGGATTTTGGCAGATTCACTGAAAAGAGGTACAAATCTATTGTCAAGTACAAGACAG
CTTTCTACTCTTTCTACCTTCCTGTACCTGCGGCCATGTACATGGTAGGAATTGATGGCGAGAAGGAGCATGCCAATGCT
TAGAAGATCCTACTGGAGATGGGAGAGTTTTTTCAAATTCAGGATGATTACCTTGACCTCTTTGGGGACCCCATTGTGAC
CGGCAAAGTTGGCACTGACATTCAGGACAACAAATGCAGCTGGCTGGTGGTTCAGTGTCCGCAGTGGTCCACTCTGGAAC
AGTATCAGATCCTGAAGGAAAATTACAGAGAGAAGAAGGCCAAGAAGGTAGTCTGGGTGAAGGCACTATATAAGGAGCTG
GATCTGCCAGCCGTGTTCTTGTAGTGCGAGGAAGACGGTTACAGCCACATTATGGGTCTCACTGAACAGTACGCAGCGCC
CCTGCTCCCAGCCATCTTTCTGGGGCTTGCGCACAAAATCTACAAGCAGAAAAAG

Alignment

ORF - retro_nleu_2595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.29 %
• Parental protein coverage: 87.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TEEPRALCSSLRMNGDQKSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPETGDAIARLKEVLEYNAIGGKY
          T...RALCSSLRMNGDQKSDVYAQEKQDF.QHFSQIV.VLTEDEMGH.ETGDAIARLKEVLEYNAIGGKY
Retrocopy TSRNRALCSSLRMNGDQKSDVYAQEKQDFFQHFSQIVGVLTEDEMGHSETGDAIARLKEVLEYNAIGGKY

Parental  HRGLAVVVAFRELVEPRKQDADSLQRAWTVGWCVELXXXXLLVADDIMDSSLTRRGQICWYQKPGVGLDA
          HRGL.V.V.F.ELVEPRKQDADSLQRA.TVGWCVEL.....LV.DDIMDSSLTR.GQIC.YQK.G.G.DA
Retrocopy HRGLTVLVVFQELVEPRKQDADSLQRALTVGWCVELLQAFFLVTDDIMDSSLTRWGQICCYQKMGMG*DA

Parental  INDANLLEACVYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLITAPQGNVDLVRFTEKRYKSIVK
          IN...LL.AC.Y.LLKLYCREQPYYLNLIELFLQ.SYQ.EIGQTLDL.TAP..NVD..RFTEKRYKSIVK
Retrocopy INYGILLQACIYYLLKLYCREQPYYLNLIELFLQISYQPEIGQTLDLTTAP*DNVDFGRFTEKRYKSIVK

Parental  YKTAFYSFYLPIAAAMYMAGIDGEKEHTNAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCS
          YKTAFYSFYLP..AAMYM.GIDGEKEH.NA.KILLEMGEFFQIQDDYLDLFGDP.VTGK.GTDIQDNKCS
Retrocopy YKTAFYSFYLPVPAAMYMVGIDGEKEHANA*KILLEMGEFFQIQDDYLDLFGDPIVTGKVGTDIQDNKCS

Parental  WLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPP
          WLVVQC.Q..T.EQYQILKENY..K.A.KV..VKALY.ELDLPAVFL..EED.YSHIM.L.EQYAAPL.P
Retrocopy WLVVQCPQWSTLEQYQILKENYREKKAKKVVWVKALYKELDLPAVFL*CEEDGYSHIMGLTEQYAAPLLP

Parental  AIFLGLARKIYKRKK
          AIFLGLA.KIYK.KK
Retrocopy AIFLGLAHKIYKQKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2595 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,