RetrogeneDB ID: retro_etel_1074

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_206893:541..1089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000005817
• Aliases: None
• Description: None

Sequence

>retro_etel_1074
GGGGAAGCTCCCGACTATGATCAAAGCCAGTGGCTGGATGTGAAATTCAAGTTAGATCTGGGCTTTCCTAATTTGCCCTA
CCTCATGGACGGGAAGAACCAGATCACTCAGAGCAATGCCATCTTGCGCTACATCGCTCGCAAGCACAATACGTGTGGCG
ACCCAGAAGAAGAGAAGATTCGAGTGGACATCATGGAGAACCAGATCATGGATTTCCGCACGCAGCTTGTCCAGATCTAC
TGCCCTGACCATGAAAAGCTGAAGCCTCAGTACCTGGAGCAGCTGCCTGGAAACCTCAAACCGTTTCCTTTGTTCCTGGG
AAATTCTCATGGTTTACTGGGGAAAACCTCACCTTCATGGACTTCCTCACCTATGCTGTGTTAGACCAGAACCGCATGTT
TGAGCCCAAGTGCCTGGATGAGTTCCCAAATCTGAAGGCTTTCACGTGTCGTTTTGAGGCCTTGGAGAAAATAGCTGCGT
ACATGCAGTCTGACCGCTTCTTCAAGCTGCCCTTGAACAAGATGGCCCAGTGGGGAAACAAGAGGTGC

Alignment

ORF - retro_etel_1074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.1 %
• Parental protein coverage: 82.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GEAPDYDRSQWLDVKFKLDLDFPNLPYLVDGKNKITQSNAILRYIARKHNMCGNTEEEKIRVDIMENQIM
          GEAPDYD.SQWLDVKFKLDL.FPNLPYL.DGKN.ITQSNAILRYIARKHN.CG..EEEKIRVDIMENQIM
Retrocopy GEAPDYDQSQWLDVKFKLDLGFPNLPYLMDGKNQITQSNAILRYIARKHNTCGDPEEEKIRVDIMENQIM

Parental  DFRMQLVRISYSPDHEKLKPQYLEQLPGNLKQFSLFLG-KFSWFAGEKLTFVDFLTYDVLDQNRMFEPKC
          DFR.QLV.I.Y.PDHEKLKPQYLEQLPGNLK.F.LFLG.KFSWF.GE.LTF.DFLTY.VLDQNRMFEPKC
Retrocopy DFRTQLVQI-YCPDHEKLKPQYLEQLPGNLKPFPLFLG<KFSWFTGENLTFMDFLTYAVLDQNRMFEPKC

Parental  LDEFPNLKAFMCRFEALEKIAEYMQSDRFFKLPINNKMALWGSKRC
          LDEFPNLKAF.CRFEALEKIA.YMQSDRFFKLP..NKMA.WG.KRC
Retrocopy LDEFPNLKAFTCRFEALEKIAAYMQSDRFFKLPL-NKMAQWGNKRC

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_1074 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074 , retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,