RetrogeneDB ID: retro_etel_1924

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_31468:606..840(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000008145
• Aliases: None
• Description: None

Sequence

>retro_etel_1924
CACAGCAAATACCTGAGTAATGAAGGAAACTTGAAACTATTTGGGATGTGCAACAATTTGAATGACATGGGCACAATTAT
AAACTTGTGGTGACAGTACCTGGACAGATTGATCTGATTACAGGATGGTTATGGATTTGACTGACCTCAGAAAGTACATA
GAGGAAGCAATTATGAAGCCCCTTGATCATAAGAATATGGATCTAGATGTCCATACTTCACAGAAATCACTTCC

Alignment

ORF - retro_etel_1924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.39 %
• Parental protein coverage: 54.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HSKYLSNEENLKLFGKCNNPNG-HGHNYKVVVTVHGEIDPATG-MVINLTDLREYMEEAIMKPLDHKNLD
          HSKYLSNE.NLKLFG.CNN.N..HGHNYK.VVTV.G.ID..TG.MV..LTDLR.Y.EEAIMKPLDHKN.D
Retrocopy HSKYLSNEGNLKLFGMCNNLND<HGHNYKLVVTVPGQIDLITG<MVMDLTDLRKYIEEAIMKPLDHKNMD

Parental  LDV-PYFADVVS
          LDV.PYF....S
Retrocopy LDV<PYFTEITS

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_1924 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 20 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003968	3 retrocopies	retro_amel_1001, retro_amel_1480, retro_amel_691,
Bos taurus	ENSBTAG00000003770	3 retrocopies	retro_btau_1182, retro_btau_1762, retro_btau_682,
Canis familiaris	ENSCAFG00000013915	2 retrocopies	retro_cfam_1386, retro_cfam_1859,
Choloepus hoffmanni	ENSCHOG00000000013	2 retrocopies	retro_chof_1925, retro_chof_2556,
Callithrix jacchus	ENSCJAG00000012437	2 retrocopies	retro_cjac_2534, retro_cjac_2853,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924 , retro_etel_2039,
Felis catus	ENSFCAG00000024702	3 retrocopies	retro_fcat_1546, retro_fcat_212, retro_fcat_564,
Homo sapiens	ENSG00000150787	1 retrocopy	retro_hsap_3408,
Myotis lucifugus	ENSMLUG00000023388	1 retrocopy	retro_mluc_946,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Nomascus leucogenys	ENSNLEG00000007299	1 retrocopy	retro_nleu_1856,
Otolemur garnettii	ENSOGAG00000017191	3 retrocopies	retro_ogar_1718, retro_ogar_2790, retro_ogar_609,
Pongo abelii	ENSPPYG00000003880	1 retrocopy	retro_pabe_432,
Pan troglodytes	ENSPTRG00000004288	3 retrocopies	retro_ptro_2315, retro_ptro_2979, retro_ptro_337,
Sorex araneus	ENSSARG00000001975	2 retrocopies	retro_sara_163, retro_sara_72,
Sus scrofa	ENSSSCG00000015040	1 retrocopy	retro_sscr_284,
Ictidomys tridecemlineatus	ENSSTOG00000013277	1 retrocopy	retro_itri_1096,
Tursiops truncatus	ENSTTRG00000010526	1 retrocopy	retro_ttru_1710,
Vicugna pacos	ENSVPAG00000000061	1 retrocopy	retro_vpac_363,