RetrogeneDB ID: retro_etel_1889

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_311941:7600..7857(-)
• 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_1889
GGTAATTTGGGAAGGAAATCCTGAAAATCACAACCTGCTGCAGCCTACTTCTGGAGGCTCTACCAGCCGAGCAGTGGCTG
GGCCGCCTAGCGGGAAAATGCCCGCTGCAGGACCTCAGCGGGCACCGGAGACATGGGGTCTTCAACACAGAAGATTCACC
TGAGCTCAAAGTTGGTCCTGTTCCAAGATTAGTAATGAGTCTCCTTCTCTTCACTTCTGTATTGATGTTGGCCATGTGGG
GCAAGTACACTCGTTCA

Alignment

ORF - retro_etel_1889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.87 %
• Parental protein coverage: 88.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRT-TSAGTGGMWR-FYTEDSPGLKVGPVPVLVMSLL
          G..GR...K...A.A......Q........R...R..TSAGTG.M...F.TEDSP.LKVGPVP.LVMSLL
Retrocopy GNLGRKS*KSQPAAAYFWRLYQPSSGWAA*RENARCRTSAGTGDMGS<FNTEDSPELKVGPVPRLVMSLL

Parental  FIASVFMLHIWGKYTRS
          ...SV.ML..WGKYTRS
Retrocopy LFTSVLMLAMWGKYTRS

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_1889 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,