RetrogeneDB ID: retro_ttru_689

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3085:333688..334591(+)
• Located in intron of: ENSTTRG00000008461

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDPS
• Ensembl ID: ENSTTRG00000013326
• Aliases: None
• Description: farnesyl diphosphate synthase [Source:HGNC Symbol;Acc:3631]

Sequence

>retro_ttru_689
AGAGTATTTTACTCCTCCCTCAGAATAGATGGAGACCAGAAATTGGACGTTTATGCAGAAAGGCAGGATTTCATCCAGCA
CTTATTCCAGATTGTCAAGGTGCTGACTGAGGAGGACACTGGGCACCCAGAGACAGGAGATGCTATTGCCCGACTCAAGG
AGGTCCTGGAGTACTGTGCCATCCGAGGCAAGTACCTTCGGGGTTTGACGGTGCTGGTAGCATTCTGGGAGCTGTCGGAG
CCCAGGAAGCAAGATGCTGACAGTCTCCGGTGGGCCATGACTGAGGGCTGGTGCGTGGAACTGCTCCAAGCCTTCCTCTT
GGTGTCAGACAACCTCATGGATGCGTTCTTCACCCGAGGGGGGCAGATCTGCTGGTATCAGAAGCCAGGCATAGGTTTGG
CTGCCATTCATGATGCTTTCCTCTTGGAGGCGTGTATCTACCGCCTGCTGAAGCTCTGCTGCTGGGAGCAGCCCTATTAC
CTGAACCTGATCGAGCTCTTCCTACAGAGTCCTTATCAGACTGAGATCGGACAGACCCTGGACCTCATCACAGCCCCCCA
GGACAGTGTGGATCTTGGCAGATTCACTGAAAAGAGGTACAGATCTATTGTCAAATACAAGACAGCTTTCTACTCCTTCT
GTCTTCCTATAGCTGCTGCCATGTATGTGGTGGACATTGACGGGAAGAAGGAGCATACCGATGCCAAGAAGATCCTGCTG
GAGATGGGAGAGTTCTTTCGGATTTAGGATGATAACCTCGATCTCTTTGGGGACCCCAGTGTGATGGGCAAGATCGGCAC
TGACATCCAGGACAACAAGTGCAGCTGGCTGGTGGCTCAGTGTTTGCCACGGGCCTCTCCGGACCAGTGCCAGATCCTGC
AGGAGAACTTTGGAGGCCGAGAA

Alignment

ORF - retro_ttru_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 71.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAFYSSLRMNGDQKLDVYAQERQDFIQHFSQIVKVLTEEDIGHPETGDAIARLKEVLEYNAVGGKYHRGL
          R.FYSSLR..GDQKLDVYA.ERQDFIQH..QIVKVLTEED.GHPETGDAIARLKEVLEY.A..GKY.RGL
Retrocopy RVFYSSLRIDGDQKLDVYA-ERQDFIQHLFQIVKVLTEEDTGHPETGDAIARLKEVLEYCAIRGKYLRGL

Parental  TVLVAFRELVEPRKQDAESLRRALTVGWCVELLQAFFVVSDDIMDSSLTRRGQICWYQKPGIGLDAINDA
          TVLVAF.EL.EPRKQDA.SLR.A.T.GWCVELLQAF..VSD..MD...TR.GQICWYQKPGIGL.AI.DA
Retrocopy TVLVAFWELSEPRKQDADSLRWAMTEGWCVELLQAFLLVSDNLMDAFFTRGGQICWYQKPGIGLAAIHDA

Parental  FLLEACVYRLLKFYCREQPYYMNLIELFLQSSYQTEIGQTLDLITAPQGNVDLGRFTEKRYKSIVKYKTA
          FLLEAC.YRLLK..C.EQPYY.NLIELFLQS.YQTEIGQTLDLITAPQ..VDLGRFTEKRY.SIVKYKTA
Retrocopy FLLEACIYRLLKLCCWEQPYYLNLIELFLQSPYQTEIGQTLDLITAPQDSVDLGRFTEKRYRSIVKYKTA

Parental  FYSFYLPVAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVMGKIGTDIQDNKCSWLVV
          FYSF.LP.AAAMY...IDG.KEH..AKKILLEMGEFF.I.DD.LDLFGDPSVMGKIGTDIQDNKCSWLV.
Retrocopy FYSFCLPIAAAMYVVDIDGKKEHTDAKKILLEMGEFFRI*DDNLDLFGDPSVMGKIGTDIQDNKCSWLVA

Parental  QCLQRASPEQRQILQENYGQKE
          QCL.RASP.Q.QILQEN.G..E
Retrocopy QCLPRASPDQCQILQENFGGRE

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_689 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_689 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 9 parental genes, and 35 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,
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,
Pongo abelii	ENSPPYG00000000747	3 retrocopies	retro_pabe_1290, retro_pabe_1329, retro_pabe_235,
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 ,