RetrogeneDB ID: retro_etel_1910

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_313592:2450..2921(-)
• 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_1910
TATGATCGAAGCCAGTGGCTGAACGTGACATTCAAGCTAGTCCTGGACTTTCCTAATTTGCCCTACCTTGTGGAGGGGAA
GAACAAGATCTCTCAGAGCAACGCCATCTTGTGCTACGTCGCTCGCAAGCACACTCTATGTGTGGCGACCCAGAGGAAGA
GAAGATTCGAGGGGATATCGCGTACAACCAGGTAATGGATTTCCACAGGCAACTTGTCCCGATCTGTACAGCCCTGACCA
TGAAAAGTTGAAGCCTCTGTACTTGGAACGGTTGCCTGGAAACCTGAAATAGTTTTCTTTGTGCCTGGGGAAATTTCGTG
GTCTGCTGGGGAAAAGCTCAACTTCGTGGACTTCCTCCCCTAGGATGCCTTAGAACAGAAGCGCATGTTTGAGCCCAAGT
GCCTGGACGAGTTCCCACATCTGAAGGCTCTCATGTGTCGTTTTGAGGCTTTGGAGAAAATAGCTGTGTAC

Alignment

ORF - retro_etel_1910 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.7 %
• Parental protein coverage: 70.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YDRSQWLDVKFKLDLDFPNL-PYLVDGKNK-ITQSNAILRYIARKHNMCGNTEEEKIRVDIMENQIMDFR
          YDRSQWL.V.FKL.LDFPNL.P.L..G..................H.MCG..EEEKIR.DI..NQ.MDF.
Retrocopy YDRSQWLNVTFKLVLDFPNL>PTLWRGRTR>LSEQRHLVLRRSQAHSMCGDPEEEKIRGDIAYNQVMDFH

Parental  MQLVRIS-YSPDHEKLKPQYLEQLPGNLKQFSLFLGKF-SWFAGEKLTFVDFLTYDVLDQNRMFEPKCLD
          .QLV.I..YSPDHEKLKP.YLE.LPGNLK.FSL.LGKF.SW.AGEKL.FVDFL..D.L.Q.RMFEPKCLD
Retrocopy RQLVPIC<YSPDHEKLKPLYLERLPGNLK*FSLCLGKF<SWSAGEKLNFVDFLP*DALEQKRMFEPKCLD

Parental  EFPNLKAFMCRFEALEKIAEY
          EFP.LKA.MCRFEALEKIA.Y
Retrocopy EFPHLKALMCRFEALEKIAVY

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_1910 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,