RetrogeneDB ID: retro_etel_2049

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_41409:449..1072(-)
• Located in intron of: None

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_2049
ATGCTACAGCTTCTAGAAAAAGTTAATTGAAATGGAACAGTGGACAGAAGGAAAAGGTGTCATTGTCCATGGGGCTAACA
ACACTTTCTCTTCGGGGTCTGATCTGAATGCTGTGAAAAGCACTGGGAACTCCAGAGGATGGAGTGGCATTATGTATGTT
CATGCAGAATACCTTAACAAGATTCACGAGACTTCCTTTAATAAGTGTTGCACTGGTTCAAGGCCGGGCAATGGGTGGAG
GAGCAGAATTTACGACAGCATGCGATTTCAGGTTAATGACTCCAGAAAGTGAGATCAGATTTGTCCATAAGGAGGTGGGT
ATAATACCAAGTTGGGGTGGCACAACCCGGCTGTTTGAAATAATTGGCAGTAGACAAGTTCTCAAGGTGTTAACTGGGGC
CCTCAAACTGGATCCCCCAAAAGCTTTAAATATAGGAATGGTTGAAGAGGTTTTACAGTCTAAAGATGCAATTCAGTCTC
TAGAAGAGGCACAAGCATGGCTACAGCAGTTTATCAAAGGGCCACCAGAAGTCATTAGAACATTGAAATTGTCTGTTTCT
TCAGTCAAAGAGTTATGCTTAGAGGAGGCATTAGAGAAAGAGAGAGATCTTTTAGAAAGTCTG

Alignment

ORF - retro_etel_2049 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.34 %
• Parental protein coverage: 67.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLQLLEKV-IELEQWTEGKGLIVHGANNTFSSGSDLNAVKS-LGTPEDGVALCMFMQNTLTRFMRLPLIS
          MLQLLEKV.IE.EQWTEGKG.IVHGANNTFSSGSDLNAVKS.LGTPEDGVALCMFMQNTLTRF.RLPLIS
Retrocopy MLQLLEKV>IEMEQWTEGKGVIVHGANNTFSSGSDLNAVKS>LGTPEDGVALCMFMQNTLTRFTRLPLIS

Parental  VALVQGRAMGGGAEFTTACDFRLMTPESEIRFVHKEMGIIPSWGGTTRLVEIIGSRQALKVLTGALKLDP
          VALVQGRAMGGGAEFTTACDFRLMTPESEIRFVHKE.GIIPSWGGTTRL.EIIGSRQ.LKVLTGALKLDP
Retrocopy VALVQGRAMGGGAEFTTACDFRLMTPESEIRFVHKEVGIIPSWGGTTRLFEIIGSRQVLKVLTGALKLDP

Parental  EKALTIGMVEEILQSKDATQSLEEAQAWLQQFIRGPPEVIRTLKSSVSSVKELCLEEALEKERDLLETV
          .KAL.IGMVEE.LQSKDA.QSLEEAQAWLQQFI.GPPEVIRTLK.SVSSVKELCLEEALEKERDLLE..
Retrocopy PKALNIGMVEEVLQSKDAIQSLEEAQAWLQQFIKGPPEVIRTLKLSVSSVKELCLEEALEKERDLLESL

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_2049 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 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,