RetrogeneDB ID: retro_etel_1056

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_205027:8342..8588(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS1
• Ensembl ID: ENSETEG00000004020
• Aliases: None
• Description: signal peptidase complex subunit 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:23401]

Sequence

>retro_etel_1056
CAGAAGTTAGCTGAACAGATGTTTCAAGAGATTTTGTTTTTTTCTGCAATAGTTGTTTATCTACGGGTACGTGACTGAAC
AGGTCGGATGGACTGTTTACATATCCATGGCTGGATTTGATTTTTCATGTTTGCTGACACGTCTTCCATGGCCCATCTAT
TGCCAGCCCCCCTCAAGTGGCTACCTAGTCATGATTCAGAAATGGAAGACAAGAAGCCAAGGGATCAAAAAATTAAGAGG
CATTCT

Alignment

ORF - retro_etel_1056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.24 %
• Parental protein coverage: 92.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKLAEQLFQVIILFSAIVG-FVYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIYRR-HPLKWLPVQDSG
          QKLAEQ.FQ.I.LF......F.YGYV.EQ.GWTVYI.MAGF.FSCLLT..PWPIY....PLKWLP..DS.
Retrocopy QKLAEQMFQEI-LFFSAIV>FIYGYVTEQVGWTVYISMAGFDFSCLLTRLPWPIYCQ<APLKWLPSHDSE

Parental  TEDKKPGDRKIKRHA
          .EDKKP.D.KIKRH.
Retrocopy MEDKKPRDQKIKRHS

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_1056 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012421	3 retrocopies	retro_dnov_2086, retro_dnov_2245, retro_dnov_698,
Dipodomys ordii	ENSDORG00000000678	4 retrocopies	retro_dord_273, retro_dord_274, retro_dord_686, retro_dord_734,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Echinops telfairi	ENSETEG00000004020	1 retrocopy	retro_etel_1056 ,
Loxodonta africana	ENSLAFG00000016073	2 retrocopies	retro_lafr_575, retro_lafr_625,
Mus musculus	ENSMUSG00000021917	2 retrocopies	retro_mmus_2758, retro_mmus_2928,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,