RetrogeneDB ID: retro_etel_1524

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_276890:157..567(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000006584
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MED29
• Ensembl ID: ENSETEG00000000406
• Aliases: None
• Description: mediator complex subunit 29 [Source:HGNC Symbol;Acc:23074]

Sequence

>retro_etel_1524
AGGACTTTGATCGCACAGCTGAAAGGAGAGCCTCCAGACTTTGATGAAGGGCCAGCTCAGATTTTGATTCAGAACACGAA
CATTGACAGCGGACCAAAGAACAAAGAAGGACCGGTACAGCGTTTCCACAAGTGCCTGGAGGAGTTCTGTGACCAGCTGG
AGCTCTGCGTGCGCCTGGCGCAAGAGTGCCTGTCCCAGAGCTGCGACAGTGCAAGCACTCTCCCACACTGGTGCCCACAG
CGACCACGCCAGACACCGTGCAGCCCTACAGCCTGCCCTACCCTCAGTACCTGGCCATCATCAAAGCCCAGATCGCCTGT
GCCAAGGGCATTCACACCGCCCTGCTGGACAGGGCCAACAAGATCAGGGGCAAGACACTGGCCCCACCTCCTGGCCCTGG
GGGCACCCTC

Alignment

ORF - retro_etel_1524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.32 %
• Parental protein coverage: 62.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KMLIPQLK-ESLQTLMKVA-AQNLIQNTNIDNGQKSSDGPIQRFDKCLEEFYALCDQLELCLRLAHECLS
          ..LI.QLK.ESLQTLMK...AQ.LIQNTNID.G.K...GP.QRF.KCLEEF...CDQLELC.RLA.ECLS
Retrocopy RTLIAQLK>ESLQTLMKGQ<AQILIQNTNIDSGPKNKEGPVQRFHKCLEEF---CDQLELCVRLAQECLS

Parental  QSCDSA-KHSPTLVPTATKPDAVQPDSLPYPQYLAVIKAQIACAKDIHTALLDCANKVTGKTPAPPTGPG
          QSCDSA.KHSPTLVPTAT.PD.VQP.SLPYPQYLA.IKAQIACAK.IHTALLD.ANK..GKT.APP.GPG
Retrocopy QSCDSA<KHSPTLVPTATTPDTVQPYSLPYPQYLAIIKAQIACAKGIHTALLDRANKIRGKTLAPPPGPG

Parental  GTL
          GTL
Retrocopy GTL

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_1524 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000000406	1 retrocopy	retro_etel_1524 ,
Mus musculus	ENSMUSG00000003444	1 retrocopy	retro_mmus_781,