RetrogeneDB ID: retro_etel_1777

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_294503:93128..93397(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC61B
• Ensembl ID: ENSETEG00000005293
• Aliases: None
• Description: Sec61 beta subunit [Source:HGNC Symbol;Acc:16993]

Sequence

>retro_etel_1777
CCCAGCGGCACTAACGTGGCCTCCTCTGGCTGCTGTCCCAGCAAAGCAGTGGTCTCCCGGGCGGGATCCACCAGCTAGCA
GAGGCAAACTGCCAGCTGCAGACCAAGGCACACAGGCCGCAAGCCCTCGGCAAGCACTGGGGGGAGGTGGCGCTTCTTCC
CACAAGATTCCCGGGGTTCACAGTTGGCACGGGTCCGGTATGGGGCATGAGTCTTCTGTTCATCACTTCTGTATTTATGT
TCAACATCTGGGGCAAGTACACTCGTTCA

Alignment

ORF - retro_etel_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.3 %
• Parental protein coverage: 94.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDS-PGLKVGPVPVL
          PSGTNV.SSG..PSKAV..RA.GST..QR..ASC..R..GR..SA.TGG.WRF...DS.PG..VG..PV.
Retrocopy PSGTNVASSGCCPSKAVVSRA-GSTS*QRQTASCRPRHTGRKPSASTGGRWRFFPQDS<PGFTVGTGPVW

Parental  VMSLLFIASVFMLHIWGKYTRS
          .MSLLFI.SVFM..IWGKYTRS
Retrocopy GMSLLFITSVFMFNIWGKYTRS

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_1777 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 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002457	3 retrocopies	retro_btau_1053, retro_btau_360, retro_btau_791,
Callithrix jacchus	ENSCJAG00000011279	1 retrocopy	retro_cjac_503,
Equus caballus	ENSECAG00000026930	1 retrocopy	retro_ecab_711,
Echinops telfairi	ENSETEG00000005293	4 retrocopies	retro_etel_1777 , retro_etel_1889, retro_etel_483, retro_etel_695,
Homo sapiens	ENSG00000106803	1 retrocopy	retro_hsap_871,
Gorilla gorilla	ENSGGOG00000004205	1 retrocopy	retro_ggor_708,
Macropus eugenii	ENSMEUG00000000321	1 retrocopy	retro_meug_1921,
Microcebus murinus	ENSMICG00000011121	4 retrocopies	retro_mmur_1037, retro_mmur_1631, retro_mmur_435, retro_mmur_543,
Myotis lucifugus	ENSMLUG00000001097	1 retrocopy	retro_mluc_2170,
Macaca mulatta	ENSMMUG00000010661	1 retrocopy	retro_mmul_86,
Mus musculus	ENSMUSG00000053317	2 retrocopies	retro_mmus_1377, retro_mmus_2679,
Nomascus leucogenys	ENSNLEG00000017055	1 retrocopy	retro_nleu_2844,
Otolemur garnettii	ENSOGAG00000004168	3 retrocopies	retro_ogar_1132, retro_ogar_2671, retro_ogar_823,
Pongo abelii	ENSPPYG00000019441	1 retrocopy	retro_pabe_680,
Pan troglodytes	ENSPTRG00000021184	1 retrocopy	retro_ptro_606,
Rattus norvegicus	ENSRNOG00000006345	1 retrocopy	retro_rnor_1589,