RetrogeneDB ID: retro_etel_1261

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_237254:646..1377(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000008637
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSETEG00000006221
• Aliases: None
• Description: serine/arginine-rich splicing factor 6 [Source:HGNC Symbol;Acc:10788]

Sequence

>retro_etel_1261
GGATACAGCAGTCAGAGAACCTCTGGCAGAGACAAATATGGACCACCTGTTTGTACAGAATACAGGCTTATTGTAGAAAA
CCTATCTAGTTGCTGCAGTTGGCAGGATGTAAAGGATTTCATGAGACAAGCAGGTGAAGTGAGCTCCTCGGATGCTCACA
AAGAACGCACAAATGAGGGTGTGATTGAGTTTCGCTCCTACTCTGACATGAAATGAGATTTGGATAAACTGGATAGCACA
GAAATAAGTGGCAGGAACATCCGGCTCTTGAAGATAAGCCGAGAACAAGCCATAGGCGCTCTTACTCTGGAAGCAGATCA
AGGTCACAATCTAGAAGAAGGTCATGAAGTAGGAGTCACAGGAGCAGCCGCAGTAGATCTCGAAGCGCTTTCAAAAGTCG
CTCCTGATCCAGGTCAAGGAGCAAAGGTTGGTCGCGTTCTCGGTCAAAAAGCAGGAAGTCTAGACCAAAGAGCAAATCTA
AGCCCAAGTCTAATCGAGCTTCCTGTTCCCGCTCTAGAAGTAGATCTAAGGATAGGTATGAAATATCTCGGAGCAGATCT
CGAAGTAGGACTCGTTCACCCAAGGAAACTGGGAAAAGTGATGTGAAGTCAAAATCCAGATCAAGGAGCCAGTCTCCATC
CGATTCACCTGTACCTGCCCCACCTTCAGAGGCTCATGCTGTGTCTCCACCAAAAAGAGCGGCATCAAGATCCCGCTCTA
GGTCTCGTTCA

Alignment

ORF - retro_etel_1261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.35 %
• Parental protein coverage: 71.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GYSSRRTSGRDKYGPPVRTEYRLIVENLSSRCSWQDLTDFMRQAGEVTYADAHKERTNEGVIEFRSYSDM
          GYSS.RTSGRDKYGPPV.TEYRLIVENLSS.CSWQD..DFMRQAGEV...DAHKERTNEGVIEFRSYSDM
Retrocopy GYSSQRTSGRDKYGPPVCTEYRLIVENLSSCCSWQDVKDFMRQAGEVSSSDAHKERTNEGVIEFRSYSDM

Parental  KRALDKLDGTEINGRNIRLI-EDKPRTSHRRSYSGSRSRSRSRRRSRSRSRRSSRSRSRSASKSRSRSRS
          K..LDKLD.TEI.GRNIRL..EDKPRTSHRRSYSGSRSRS.SRRRS.SRS.RSSRSRSRSA.KSRS.SRS
Retrocopy K*DLDKLDSTEISGRNIRLL<EDKPRTSHRRSYSGSRSRSQSRRRS*SRSHRSSRSRSRSAFKSRS*SRS

Parental  RSKGRSRSRSKSRKSRSKSKSKPKSDRASRSRSRSRSKDKYEKSRSRSRSRSRSPKENGKSDVKSKSRSR
          RSKG.SRSRSKSRKSR.KSKSKPKS.RAS.SRSRSRSKD.YE.SRSRSRSR.RSPKE.GKSDVKSKSRSR
Retrocopy RSKGWSRSRSKSRKSRPKSKSKPKSNRASCSRSRSRSKDRYEISRSRSRSRTRSPKETGKSDVKSKSRSR

Parental  SQSRSNSPVPAPPSKAHSVSPPKRAASRSRSRSRS
          SQS.S.SPVPAPPS.AH.VSPPKRAASRSRSRSRS
Retrocopy SQSPSDSPVPAPPSEAHAVSPPKRAASRSRSRSRS

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_1261 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002061	1 retrocopy	retro_acar_191,
Echinops telfairi	ENSETEG00000006221	1 retrocopy	retro_etel_1261 ,
Echinops telfairi	ENSETEG00000010117	2 retrocopies	retro_etel_2064, retro_etel_445,
Homo sapiens	ENSG00000124193	1 retrocopy	retro_hsap_1809,
Gorilla gorilla	ENSGGOG00000009808	1 retrocopy	retro_ggor_2176,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697,
Nomascus leucogenys	ENSNLEG00000006524	1 retrocopy	retro_nleu_1294,
Oryctolagus cuniculus	ENSOCUG00000009785	1 retrocopy	retro_ocun_312,
Pongo abelii	ENSPPYG00000011019	1 retrocopy	retro_pabe_1483,
Pan troglodytes	ENSPTRG00000013506	1 retrocopy	retro_ptro_3057,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
Tursiops truncatus	ENSTTRG00000015410	2 retrocopies	retro_ttru_1786, retro_ttru_1787,