RetrogeneDB ID: retro_etel_564

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_908:15501..16405(-)
• Located in intron of: ENSETEG00000004197

Retrocopy information

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

Parental gene information

• Parental gene symbol: ECHDC1
• Ensembl ID: ENSETEG00000006454
• Aliases: None
• Description: enoyl CoA hydratase domain containing 1 [Source:HGNC Symbol;Acc:21489]

Sequence

>retro_etel_564
AAAATGGCATCTAGTGTTTTGAAGACATCATCTCTGTCTGCCCGGACAAAACTGCTGTGTCAGACTGGGTTGTCACTTTA
TAATACATCTCATGGCTTCCATGAGGAAGAAGTTTAAAAAGAGCTTGTACAGTTTACTGGTGGATTCGTTGAACTTCAGA
AGAACGATAATGGCATTGACATTCTTACTCTGAATAATTAAGTAAAATGAATGCATTCTCAGGTGTTAAGATGCTACAGC
TACTAGAAAATGTAATTGAATTGGAACAATGGACAGAAGGAAAAGGTTTCATTGTCCATGGGGCTAACAACACTTTCTCT
TCGGGGTCTGATCTGAATGCTGTGAAAGCACTAGGAACTCCAGAGGATGGAGTGGCATTATGTATGTTCATGCAGAATAC
CTTAACAAGATTCATGAGACTTCCTTTAATAAGTGTTGCACTGGTTCAAGGCCGGGCAATGGGTGGAGGAGCAGAATTTA
CTACAGCATGCGATTTCAGGTTAATGACTCCAGAAAGTGAGATCAGATTTGTCCATAAGGAGATGGGTATAATACCAAGT
TGGGGTGGCACAACCCGGCTGGTTGAAATAATCGGCAGTAGATAAGCTCTCAAGGTGTTAACTGGGGCCCTCAAACTGGA
TCCCCAAAAAGCTTTAACTATAGAAATGGTTGAAGAGATCTTACAGTCTAAGATGCAACTCAGTCTCTAGAAGAGGCACA
AGCATGGCTACAGCAGTTTATAAGAGGGCCACCAGAAGTCATTAGAACATTGAAATTGTCTGTTTCCTCAGTCAAAGAGT
TATGCTTAGAGGAGGCATTAGAGAAAGAGAGAGATCTTTTAGAAGCAGTCTGGGGTGGACCTGCAAATCTAGCGGCAATT
TCTAAGAGAGAGAAATTTAACAAA

Alignment

ORF - retro_etel_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.43 %
• Parental protein coverage: 98.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EMAASVLKTPSLSARTKLLCQTGLSLYNTSHGFHEEEVKKKLVQFTGGSVDLQKNDNGIGILTLNN-PSK
          .MA.SVLKT.SLSARTKLLCQTGLSLYNTSHGFHEEEV.K.LVQFTGG.V.LQKNDNGI.ILTLNN..SK
Retrocopy KMASSVLKTSSLSARTKLLCQTGLSLYNTSHGFHEEEV*KELVQFTGGFVELQKNDNGIDILTLNN<LSK

Parental  MNAFC-VMMLQLLEKVIELEQWTEGKGLIVHGANNTFSSGSDLNAVKSLGTPEDGVALCMFMQNTLTRFM
          MNAF..V.MLQLLE.VIELEQWTEGKG.IVHGANNTFSSGSDLNAVK.LGTPEDGVALCMFMQNTLTRFM
Retrocopy MNAFSGVKMLQLLENVIELEQWTEGKGFIVHGANNTFSSGSDLNAVKALGTPEDGVALCMFMQNTLTRFM

Parental  RLPLISVALVQGRAMGGGAEFTTACDFRLMTPESEIRFVHKEMGIIPSWGGTTRLVEIIGSRQALKVLTG
          RLPLISVALVQGRAMGGGAEFTTACDFRLMTPESEIRFVHKEMGIIPSWGGTTRLVEIIGSR.ALKVLTG
Retrocopy RLPLISVALVQGRAMGGGAEFTTACDFRLMTPESEIRFVHKEMGIIPSWGGTTRLVEIIGSR*ALKVLTG

Parental  ALKLDPEKALTIGMVEEILQSK-DATQSLEEAQAWLQQFIRGPPEVIRTLKSSVSSVKELCLEEALEKER
          ALKLDP.KALTI.MVEEILQSK.DATQSLEEAQAWLQQFIRGPPEVIRTLK.SVSSVKELCLEEALEKER
Retrocopy ALKLDPQKALTIEMVEEILQSK<DATQSLEEAQAWLQQFIRGPPEVIRTLKLSVSSVKELCLEEALEKER

Parental  DLLETVWGGPANLAAIAKREKFNK
          DLLE.VWGGPANLAAI.KREKFNK
Retrocopy DLLEAVWGGPANLAAISKREKFNK

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_564 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001069	1 retrocopy	retro_cfam_2182,
Cavia porcellus	ENSCPOG00000004786	1 retrocopy	retro_cpor_1303,
Echinops telfairi	ENSETEG00000006454	2 retrocopies	retro_etel_2049, retro_etel_564 ,
Mustela putorius furo	ENSMPUG00000014606	1 retrocopy	retro_mputfur_14,
Sorex araneus	ENSSARG00000011144	2 retrocopies	retro_sara_149, retro_sara_255,