RetrogeneDB ID: retro_etel_730

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_156116:934..1817(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDPS
• Ensembl ID: ENSETEG00000001154
• Aliases: None
• Description: farnesyl diphosphate synthase [Source:HGNC Symbol;Acc:3631]

Sequence

>retro_etel_730
AGAACGTGTTGCTCCTCTCTCAGAATGAACGGAGACCAGAAAGCGGATGCTCACGCCCAAGAAAAGCAGAATTTCACCCA
GCACTTCTCCCATGTGTTCAAAGTGCTGACTGAGGATGAGCTGGGCCCCCAGAGATGGGAGACGCTGTTGCCCGGCTCAG
GAAGGTCCTGGAGTACAATGTCCTCGGAGGCAAGTACAGCCGAGGGGTGACAGTGGTGGCTGTGTTCCAGGCGCTGGTGG
AGCCCAGGAAGCAGGATGCTGACAGTCTGCAGCGGGCCCTGACCTTGGGCTGGTGGGTCGAGTTGCTCCAAGCTTTCCTC
CTGATACTGGATGACATAATGGATTCATCTCTCACCCGCCGGGGGCAGCCCTGCTGGTACCAGAAGCCAGGCATAGGTCT
GGATGCCATCAATGACGCCAGGCTGCTGGAATCCTCTATCTACCACCTGTTGAAGTTCTACTGCCGGGGGCAGCCCTACT
ACCTGCACCTACTCGAGCTCTCCCTGGAGAGTTCCTATCAGACTGAGATAGGACAGACCCTGGACCTCATCACTGCCCCC
CAGGGCAAGGTGGATCTCAGCAGGTTGACCCCAAAGAGGTACAAATCCATAGTCAAGTAAAGGCCTCGTTCTACTCCTTT
TACCACCCCATCGCTGCTGCCATGTACATGACGGGCATTGACGGGGAGAAGGAGCATGCTGATGCCAAGCGGATCCTGCT
GGAGATGGGCGAGTACTTTCAGATCCAGGATGATTACCTGGACCTCTTTGGGGACCCTAGTGTGACAGACAAGGTTGGCA
CTGACATCCAGGACAACAAATGCAACTGGCTGGTGGTTCAGTGTCTGCAGCAGGCCTCTCCAGACCAGCGCCAGGTCCTG
CAG

Alignment

ORF - retro_etel_730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.21 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RAFCSSLRMNGDQKVDAYAQEKENFIQHFSHVLKVLVEDDLGH-PETGDAVARLKKVLEYNVIGGKYNRG
          R..CSSLRMNGDQK.DA.AQEK.NF.QHFSHV.KVL.ED.LG..PE.GDAVARL.KVLEYNV.GGKY.RG
Retrocopy RTCCSSLRMNGDQKADAHAQEKQNFTQHFSHVFKVLTEDELGP<PEMGDAVARLRKVLEYNVLGGKYSRG

Parental  MTVVAVFQALAEPGQQDADSLQRALTVGWCVELLQAFLLILDDIMDSSLTRRGQPCWYQKPGIGLDAIND
          .TVVAVFQAL.EP..QDADSLQRALT.GW.VELLQAFLLILDDIMDSSLTRRGQPCWYQKPGIGLDAIND
Retrocopy VTVVAVFQALVEPRKQDADSLQRALTLGWWVELLQAFLLILDDIMDSSLTRRGQPCWYQKPGIGLDAIND

Parental  AMLLESSIYRLLKFYCRGQPYYLNLMELFLESSYQTEIGQTLDLITAPQGNVDLSRFTPKRYKSIVK-YK
          A.LLESSIY.LLKFYCRGQPYYL.L.EL.LESSYQTEIGQTLDLITAPQG.VDLSR.TPKRYKSIVK..K
Retrocopy ARLLESSIYHLLKFYCRGQPYYLHLLELSLESSYQTEIGQTLDLITAPQGKVDLSRLTPKRYKSIVK<VK

Parental  TSFYSFYHPVAAAMYMAGIDGEKEHADAKRILLEMGEYFQIQDDYLDLFGDPSVTGKVGTDIQDNKCSWL
          .SFYSFYHP.AAAMYM.GIDGEKEHADAKRILLEMGEYFQIQDDYLDLFGDPSVT.KVGTDIQDNKC.WL
Retrocopy ASFYSFYHPIAAAMYMTGIDGEKEHADAKRILLEMGEYFQIQDDYLDLFGDPSVTDKVGTDIQDNKCNWL

Parental  VVQCLQRASPEQRRVLQ
          VVQCLQ.ASP.QR.VLQ
Retrocopy VVQCLQQASPDQRQVLQ

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_730 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 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,