RetrogeneDB ID: retro_etel_601

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_101875:1813..3187(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000011824
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLPTM1
• Ensembl ID: ENSETEG00000020367
• Aliases: None
• Description: cleft lip and palate associated transmembrane protein 1 [Source:HGNC Symbol;Acc:2087]

Sequence

>retro_etel_601
GAGCACTTCGCTGAGCTCGACATCCCCCAGAGCGTCCAGCAGAATGTCTCCATCTACATCCACGTCTACTTCACCAAGAG
CGGCTTCCACCCAGACCCCCAGCAGAAGGCCCTGTACCGCCGGCTTGCCACGGTCCACACATCCCGCATGATCAACAAAT
ACAAGCGCAGGCGGTTCCAGAAAACCAAGAATCTGTTGACGGGAGAGACAGAAGCCGACCCGGAAATGATCAAGAGGGCC
GAGGACTTCGGACCCGTGGAGGTCATCTCCCACTGGCACCCCAACATCACCATCAACATCGTGGACGACCACACGCCGTG
GGTGAAGGGCAGCATGCCCCCACCACTGGACCAGTACGTGAAGTTTGACGCGGTGAGCGGCGATTACTACCCCATCATCT
ACTTCAACGACTACTGGAACCTGCAGAAGGACTACTACCCCATCAACGAGAGCTTGGCCAGCCTGCCGCTGCGCGTCTCC
TTCTGCCCACTCTCGCTGTGGCGCTGGCAGCTCTACGCTGCCCAGAGCACCAAGTCACCCTGGAACTTCCTGGGCGACGA
GCTGTATGAGCAGTCGGATGAGGAGCAGGATTCGGTGAAGGTGGCCCTCCTGGAGACCAACCCTTACCTGCTGGCCCTCA
CCATCATCGTCTCCATTGTCCACAGCGTCTTTGAGTTCCTGGCCTTCAAGAACGACATCCAGTTCTGGAACAGCCGGCAG
TCCCTGGAGGGCCTGTCCGTACGCTCCGTCTTCTTCGGAGTCTTCCAGTCCCTGGTGGTCCTGCTCTACATCCTCGACAG
CGAGACCAACTTCGTGGTGCAGGTCAGTGTCTTCATCGGGGTCCTCATCGACCTCTGGAAGATCACCAAGGTCATGGATG
TCCGGCTGGATCGGGAACACAAACTGGCGGGGATCTTCCCTCGCCTGACCTTCAAGAACAAGTCCACGTACGTCGAGTCC
TCGACCAAAGTATATGATGACATGGCATTCCGTTACCTCTCGTGGATCCTCTTCCCACTCCTGGGCTGCTACGCCGTCTA
CAGCCTGCTGTACCTAGAGCACAAGGGCTGGTACTCCTGGGTGCTCAGCATGCTCTACGGCTTCCTGCTGACCTTCGGCT
TCATCACAATGATGCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCCCACCTGCCCTGGCGCATGCTCACCTAC
AAGGCCCTCAACACCTTCATGGACGACTTGTTTGCCTTTGTCATCAAGATGCCCGTGATGTACCGGATCGGCTGCCTGCG
GGACGATGTGGTTTTCTTCATCTACCTCTACCAACGGTGGATCTACCGCGTCGACCCCACACGGGTGAACAAATTTGGCA
TGAGCGGAGAGGAC

Alignment

ORF - retro_etel_601 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.79 %
• Parental protein coverage: 65.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EHFAELDIPQSVQQNGSIYIHVYFTKSGFHPDPQQKALYRRLATVHTSRMINKYKRRRFQKTKNLLTGET
          EHFAELDIPQSVQQN.SIYIHVYFTKSGFHPDPQQKALYRRLATVHTSRMINKYKRRRFQKTKNLLTGET
Retrocopy EHFAELDIPQSVQQNVSIYIHVYFTKSGFHPDPQQKALYRRLATVHTSRMINKYKRRRFQKTKNLLTGET

Parental  EADPEMIKRAEDFGPVEVISHWHPNITINIVDDHTPWVKGSVPPPLDQYVKFDAVSGDYYPIIYFNDYWN
          EADPEMIKRAEDFGPVEVISHWHPNITINIVDDHTPWVKGS.PPPLDQYVKFDAVSGDYYPIIYFNDYWN
Retrocopy EADPEMIKRAEDFGPVEVISHWHPNITINIVDDHTPWVKGSMPPPLDQYVKFDAVSGDYYPIIYFNDYWN

Parental  LQKDYYPINESLASLPLRVSFCPLSLWRWQLYAAQSTKSPWNFLGDELYEQSDEEQDSVKVALLETNPYL
          LQKDYYPINESLASLPLRVSFCPLSLWRWQLYAAQSTKSPWNFLGDELYEQSDEEQDSVKVALLETNPYL
Retrocopy LQKDYYPINESLASLPLRVSFCPLSLWRWQLYAAQSTKSPWNFLGDELYEQSDEEQDSVKVALLETNPYL

Parental  LALTIIVSIVHSVFEFLAFKNDIQFWNSRQSLEGLSVRSVCFGVLQSLVVLLYILDNETXXXXXXXXXXX
          LALTIIVSIVHSVFEFLAFKNDIQFWNSRQSLEGLSVRSV.FGV.QSLVVLLYILD.ET...........
Retrocopy LALTIIVSIVHSVFEFLAFKNDIQFWNSRQSLEGLSVRSVFFGVFQSLVVLLYILDSETNFVVQVSVFIG

Parental  XXXXXXXXXKVMDVPLNREHKLTEIFPRLTFKDKSTYVESSTKVYDDMAFRYLSWILFPLLGCYAVYSLL
          .........KVMDV.L.REHKL..IFPRLTFK.KSTYVESSTKVYDDMAFRYLSWILFPLLGCYAVYSLL
Retrocopy VLIDLWKITKVMDVRLDREHKLAGIFPRLTFKNKSTYVESSTKVYDDMAFRYLSWILFPLLGCYAVYSLL

Parental  YLEHKGWYSWVLSMLYGFLLTFGFITMTPQLFINYKLKSVAHLPWRMLTYKALNTFIDDLFAFVIKMPVM
          YLEHKGWYSWVLSMLYGFLLTFGFITM.PQLFINYKLKSVAHLPWRMLTYKALNTF.DDLFAFVIKMPVM
Retrocopy YLEHKGWYSWVLSMLYGFLLTFGFITMMPQLFINYKLKSVAHLPWRMLTYKALNTFMDDLFAFVIKMPVM

Parental  YRIGCLRDDVVFFIYLYQRWIYRVDPTRVNEFGMSGED
          YRIGCLRDDVVFFIYLYQRWIYRVDPTRVN.FGMSGED
Retrocopy YRIGCLRDDVVFFIYLYQRWIYRVDPTRVNKFGMSGED

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_601 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000020367	1 retrocopy	retro_etel_601 ,