RetrogeneDB ID: retro_etel_788

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_164380:0..688(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000004241
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STK40
• Ensembl ID: ENSETEG00000005701
• Aliases: None
• Description: serine/threonine kinase 40 [Source:HGNC Symbol;Acc:21373]

Sequence

>retro_etel_788
ACAGAGGCCAGCCGGATGGTGAGGAAGATGAAGAAGCGCATCTGCCTGGTCCTCGACTGCCTCTGTGCACACGACTTCAG
CGACAAGACCGCCGACCTGATCAACCTGCAGCACTACGTCATCAAGGAGAAGCGGCTCAGCGAGCGGGAGACCGTGGTCA
TCTTCTACGATGTGGTACGCGTGGTGGAGGCCCTGCACCAGAAAAACATTGTGCACCGAGACCTGAAGCTCGGGAACATG
GTGCTCAATAAGAGGACTCATTGGATAACCGTCACCAACTTCTGCCTCGGTAGCATCTCGTGAGCGAGGGGGATCTCCTG
AAGGACCAGAGGGGCAGCCCCGCGTACATCAGCCCCGACGTGCTCAATGGCCGGCCGTACCGGGGCAAGCCGAGCGATGT
GTGGGCCCTGGGCGTGGTACTCTTCACCATAGCTGTATGGCCAGTTCCCCTTCTACGACAGCATCCCGCAGGAGCTCTTC
CGCAAGATCAAGGCCGCCGAGTACACCATCCCCGAGGACGGGCGAGTTTCCGAGAACACCTTGTGTCTTATCTGGAAGCT
GCTGGTGCTTGACCCCCAGCAGCGCCTGGCCGCCTCTGACGTCCTGGAGGCCCTCAGCAAACATCATCGCGTCCTGGCAG
TCCCTGTCGTCTCCTGAGCGGAACCGTTTGCAAGTGGTTCCGGACATC

Alignment

ORF - retro_etel_788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 52.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TEASRMVRKMKKRICLVLDCLCAHDFSDKTADLINLQHYVIKEKRLSERETVVIFYDVVRVVEALHQKNI
          TEASRMVRKMKKRICLVLDCLCAHDFSDKTADLINLQHYVIKEKRLSERETVVIFYDVVRVVEALHQKNI
Retrocopy TEASRMVRKMKKRICLVLDCLCAHDFSDKTADLINLQHYVIKEKRLSERETVVIFYDVVRVVEALHQKNI

Parental  VHRDLKLGNMVLNKRTHRITVTNFCLGK-HLVSEGDLLKDQRGSPAYISPDVLSGRPYRGKPSDMWALGV
          VHRDLKLGNMVLNKRTH.ITVTNFCLG..HLVSEGDLLKDQRGSPAYISPDVL.GRPYRGKPSD.WALGV
Retrocopy VHRDLKLGNMVLNKRTHWITVTNFCLGS<HLVSEGDLLKDQRGSPAYISPDVLNGRPYRGKPSDVWALGV

Parental  VLFTM-LYGQFPFYDSIPQELFRKIKAAEYTIPEDGRVSENTVCLIRKLLVLDPQQRLAASDVLEALSA-
          VLFT..LYGQFPFYDSIPQELFRKIKAAEYTIPEDGRVSENT.CLI.KLLVLDPQQRLAASDVLEALS..
Retrocopy VLFTI>LYGQFPFYDSIPQELFRKIKAAEYTIPEDGRVSENTLCLIWKLLVLDPQQRLAASDVLEALSK>

Parental  IIASWQSLSSLS-GPLQVVPDI
          IIASWQSLSS.....LQVVPDI
Retrocopy IIASWQSLSSPERNRLQVVPDI

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_788 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	ENSETEG00000005701	1 retrocopy	retro_etel_788 ,