RetrogeneDB ID: retro_etel_2064

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_45604:5152..5448(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF3
• Ensembl ID: ENSETEG00000010117
• Aliases: None
• Description: serine/arginine-rich splicing factor 3 [Source:HGNC Symbol;Acc:10785]

Sequence

>retro_etel_2064
GAGCTAGATGGGCGAGTCTTGTGTGGCTGCCCTGTTTGGGTGCAACTGTCAAAGGGTAAAAGAGAAGTCAGACTATGGAT
CCACCTCTCCCTTGGGGTCATTGTCCGCAAGATGTTTATTTTGCATAAGTAAAAGAAGCCTTCCACAGATCTCCAAGAAG
GAGAAACTTCTCCTGCAGCCAGGACAGGTCCCTTTCTAGAGAGAGGAGAAGAGGGAGCTCATGGTCTCAGGAGAGAAAGC
ATAAGCTGTCCAGAACCTGCTCTAGGTCTCGTAGCGAATCTAGGTCAAAATTAAGG

Alignment

ORF - retro_etel_2064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.0 %
• Parental protein coverage: 60.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELDGRTLCGCRVRVELSNGE-KRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDR
          ELDGR.LCGC.V.V.LS.G..KRS....PP..WG..P.D.Y.........RSPRRR.FS.S..RSLSR.R
Retrocopy ELDGRVLCGCPVWVQLSKGK<KRSQTMDPPLPWGHCPQDVYFA*VKEAFHRSPRRRNFSCSQDRSLSRER

Parental  RRERSLSRERNHKPSRSFSRSRSRSRSNER
          RR..S.S.ER.HK.SR..SRSRS.SRS..R
Retrocopy RRGSSWSQERKHKLSRTCSRSRSESRSKLR

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_2064 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 10 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016062	5 retrocopies	retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
Echinops telfairi	ENSETEG00000006221	1 retrocopy	retro_etel_1261,
Echinops telfairi	ENSETEG00000010117	2 retrocopies	retro_etel_2064 , retro_etel_445,
Loxodonta africana	ENSLAFG00000018193	2 retrocopies	retro_lafr_1219, retro_lafr_80,
Myotis lucifugus	ENSMLUG00000010671	6 retrocopies	retro_mluc_1205, retro_mluc_1312, retro_mluc_1554, retro_mluc_2283, retro_mluc_278, retro_mluc_51,
Macaca mulatta	ENSMMUG00000014306	4 retrocopies	retro_mmul_1007, retro_mmul_1042, retro_mmul_1642, retro_mmul_2359,
Mus musculus	ENSMUSG00000071172	9 retrocopies	retro_mmus_100, retro_mmus_1347, retro_mmus_1749, retro_mmus_2294, retro_mmus_2337, retro_mmus_2433, retro_mmus_2654, retro_mmus_2933, retro_mmus_3629,
Otolemur garnettii	ENSOGAG00000000502	6 retrocopies	retro_ogar_1850, retro_ogar_1959, retro_ogar_2131, retro_ogar_2783, retro_ogar_597, retro_ogar_803,
Sus scrofa	ENSSSCG00000001564	1 retrocopy	retro_sscr_1038,
Ictidomys tridecemlineatus	ENSSTOG00000014280	5 retrocopies	retro_itri_123, retro_itri_502, retro_itri_664, retro_itri_857, retro_itri_901,