RetrogeneDB ID: retro_etel_941

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_188278:2466..3502(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000017337
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LRFN4
• Ensembl ID: ENSETEG00000009176
• Aliases: None
• Description: leucine rich repeat and fibronectin type III domain containing 4 [Source:HGNC Symbol;Acc:28456]

Sequence

>retro_etel_941
CCGGGCGCCTTCGCCCAGCTCGGCCAGCTCTCCCGCCTCGACCTCACCTCCAACCACCTGGCCACGTTGGCACCTGACCC
GCTCTTCTCGCATGGTCCGGACGCGGTGGCATGCCCTGCTCCGCTGGTGCTTAGCTTCAGCGGGAACCCGCTGCACTGCA
ACTGCGAGCTACTGTGGCTGGGCAGCTGGCACGGCCTGACCACCTGGAGACATGCGCTTAGCTGACCTGGCTGGCTGCTA
CTTCTGGGCCTTACCTGAGGGCGAGTCCTCCTGCGAGCCGCCCCTCATTGCCTGCCACACGCAGCGCCTCTGGGTGCTGG
AGGGCCAGCGGGCCACGCTGCGGTGCCCGGCCCTGGGCGACCCCACGGCCACCATGCATTGGGTCGGCCCTGATGACCGG
CTGGTCAGCAACTCCTCCCGGGCCCATACCTTCCCCAATGGGACCCTGGAGTTCGGGGTGACTGCTGCTGGGGCCGCGGG
GGACAACACCTGTATTGCTACCAACCCTGCTGGCGAGGCCACGGCGCGAGTGGAGCTGCGGGTGCTGGCCCTGCCCCACG
GCAGGCACAGCAGCACCGAGGGTGACCACCCGGGGCCCTTGGACATCGCCTCCTCGGCTCGCACTGCTGCCAAGGTCGAT
GGGGCGCAAGAGACCGAAGCAGCCGTGCAGGTGACAGAGGTGACCCCCGCCTCGGGGCTGGAGAACTGGGGTCCCGGACG
GCCAGCGGAGCCTGTGTGGATGTTCCAGATCCAGTACAACAGCAGTAAGGACGAAGCGCTCATCTACCGGATCGTCCCTG
CCTCCAGCCACCACTTTCTACTGAAGCACCTGGTTCCCAGTGCGGACTATGACCTCTGCCTGCTGGCCCTGTCGCCGGCC
GCTGGGCCCTCTGACCTCACGGCCACCAGGCTGCTGAGCTGTGCCCACTTCTCCACGCTGCCAGTCACACCTTTGTGCCA
TGCCCTGCAGGCCCACGTGCTGGGCGGGACCCTGACTGTGGCTGTGGGCGGCGTGCTGGTGGCCGCCTTGCTGGTC

Alignment

ORF - retro_etel_941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.28 %
• Parental protein coverage: 54.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PGAFSQLGQLSRLDLTSNRLATLAPDPLFSRGRDAEASPAPLVLSFSGNPLHCNCELLWL-RRLARPDDL
          PGAF.QLGQLSRLDLTSN.LATLAPDPLFS.G.DA.A.PAPLVLSFSGNPLHCNCELLWL...LARPD.L
Retrocopy PGAFAQLGQLSRLDLTSNHLATLAPDPLFSHGPDAVACPAPLVLSFSGNPLHCNCELLWL<GQLARPDHL

Parental  ETCASPPGLA---GRYFWAVPEGEFSCEPPLIARHTQRLWVLEGQRATLRCRALGDPTP-TMHWVGPDDR
          ETCA....LA...G.Y..A.P.......P....R.....W...G.R.....R....P.P.TMHWVGPDDR
Retrocopy ETCA*LTWLAATSGPYLRASPPASRPSLP--ATRSASGCWRASGPRC--GARPWATPRP<TMHWVGPDDR

Parental  LVGNSSRARAFPNGTLELGVTGAGDAGDYTCIATNPAGEATARVELRVLALPHGGNGSTEGGRPGPSDIA
          LV.NSSRA..FPNGTLE.GVT.AG.AGD.TCIATNPAGEATARVELRVLALPHG...STEG..PGP.DIA
Retrocopy LVSNSSRAHTFPNGTLEFGVTAAGAAGDNTCIATNPAGEATARVELRVLALPHGRHSSTEGDHPGPLDIA

Parental  ASARTAAEAEGTQETEAAVQVTEVTATSGLVSWGPGRPAEPVWMFQIQYNSSEDEALIYRIVPASPHHFL
          .SARTAA...G.QETEAAVQVTEVT..SGL..WGPGRPAEPVWMFQIQYNSS.DEALIYRIVPAS.HHFL
Retrocopy SSARTAAKVDGAQETEAAVQVTEVTPASGLENWGPGRPAEPVWMFQIQYNSSKDEALIYRIVPASSHHFL

Parental  LKHLVLGADYDLCLLALSPVAGPSDLPATRLLGCAHFSTLPPQLWCHALQAHVLGWTLTVAVGGLLVAAL
          LKHLV..ADYDLCLLALSP.AGPSDL.ATRLL.CAHFSTLP....CHALQAHVLG.TLTVAVGG.LVAAL
Retrocopy LKHLVPSADYDLCLLALSPAAGPSDLTATRLLSCAHFSTLPVTPLCHALQAHVLGGTLTVAVGGVLVAAL

Parental  LV
          LV
Retrocopy LV

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_941 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009176	1 retrocopy	retro_etel_941 ,