RetrogeneDB ID: retro_etel_125

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_2329:37691..38278(-)
• Located in intron of: ENSETEG00000004941

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDNEP1
• Ensembl ID: ENSETEG00000004654
• Aliases: None
• Description: CTD nuclear envelope phosphatase 1 [Source:HGNC Symbol;Acc:19085]

Sequence

>retro_etel_125
CTTTATCCCTGGTCCCGGAATCGGCTAGGCCAAGTGAAAATGAAGATCCTGGTACTATATCTGGATGGGACACTTATTCA
CTCACACCATGACAGGGTTGTGAGGCCCACAGTCCACCATGGACCACCTCTTGACTTCACCCTCAAGGTGGTAATACACA
AACATCCTGTCCAGTTTTTCATACATAAGAGGCCTCACGTGGATTTCTTCTTAGAAGTGATGAGCCAATGGTATGAGCTA
GTGGTGTTCACACCACGCATGAAAATTTATGGCTCTGCTGTGGCAGACACACTGGACAACAGCAGAAGCATTCTCAAGAG
GAGGTACTATAGACAGCACTGCACTTTGGAGCTGGGCAGCTACATTAAGGACCTCTTGTGGTCCACAGTGACCTCTCCAG
CATTGTGATCTGAAACTCCCCAGGGGCTTACAAGAACCATCCAGACAATGCCATTCCCATCAAGTCCTGGTTCAGTGATC
TCAGTGACACGGCTCTTCTCAACCTGCTCCCAATGCTAGATACCCTCAGGTTCACCACTGATGTTCGTTCTGTGCTGAGT
CTAAACGTTCACCAACATAGGCTCTGG

Alignment

ORF - retro_etel_125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.34 %
• Parental protein coverage: 93.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSPVSRNRLGQVKKKILVLDLDETLIHSHHDGVLRPTVRPGTPPDFILKVVIDKHPVRFFVHKRPHVDFF
          L.P.SRNRLGQVK.KILVL.LD.TLIHSHHD.V.RPTV..G.P.DF.LKVVI.KHPV.FF.HKRPHVDFF
Retrocopy LYPWSRNRLGQVKMKILVLYLDGTLIHSHHDRVVRPTVHHGPPLDFTLKVVIHKHPVQFFIHKRPHVDFF

Parental  LEVVSQWYELVVFTASMEIYGSAVADKLDNSRSILKRRYYRQHCTLELGSYIKDL-SVVHSDLSSIVILD
          LEV.SQWYELVVFT..M.IYGSAVAD.LDNSRSILKRRYYRQHCTLELGSYIKDL..VVHSDLSSIVI..
Retrocopy LEVMSQWYELVVFTPRMKIYGSAVADTLDNSRSILKRRYYRQHCTLELGSYIKDL<LVVHSDLSSIVI-*

Parental  NSPGAYRSHPDNAIPIKSWFSDPSDTALLNLLPMLDALRFTADVRSVLSRNLHQHRLW
          NSPGAY..HPDNAIPIKSWFSD.SDTALLNLLPMLD.LRFT.DVRSVLS.N.HQHRLW
Retrocopy NSPGAYKNHPDNAIPIKSWFSDLSDTALLNLLPMLDTLRFTTDVRSVLSLNVHQHRLW

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_125 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019443	1 retrocopy	retro_btau_915,
Dasypus novemcinctus	ENSDNOG00000013673	2 retrocopies	retro_dnov_1802, retro_dnov_2494,
Echinops telfairi	ENSETEG00000004654	1 retrocopy	retro_etel_125 ,
Homo sapiens	ENSG00000175826	2 retrocopies	retro_hsap_2687, retro_hsap_3188,
Gorilla gorilla	ENSGGOG00000013777	2 retrocopies	retro_ggor_1338, retro_ggor_1874,
Macaca mulatta	ENSMMUG00000010547	1 retrocopy	retro_mmul_2011,
Mus musculus	ENSMUSG00000018559	1 retrocopy	retro_mmus_1023,
Otolemur garnettii	ENSOGAG00000004389	1 retrocopy	retro_ogar_1001,
Pongo abelii	ENSPPYG00000007902	2 retrocopies	retro_pabe_2294, retro_pabe_2645,
Pan troglodytes	ENSPTRG00000008668	2 retrocopies	retro_ptro_1814, retro_ptro_2256,
Drosophila melanogaster	FBgn0029067	1 retrocopy	retro_dmel_18,