RetrogeneDB ID: retro_etel_1794

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_297731:9556..10203(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPDU1
• Ensembl ID: ENSETEG00000018609
• Aliases: None
• Description: mannose-P-dolichol utilization defect 1 [Source:HGNC Symbol;Acc:7207]

Sequence

>retro_etel_1794
ATGACAGCCGAGGAACACGGCGTGCTGAAGCGGGCTCTCGTGCCGCTGCTGCTACCTGAGAAATGCTATGACCGGCTGTT
CATCCAGTGGGACTTGCTGCACGTCTCTTGCCTCCAGATTCTCCTTAGCAAAGGCCTGGGGCTGGGCATTGTATTCACTT
CCCTGCTGGTAAAACTGCCCCAGGTGTTTAAAATCCCGGGCCGCCAAGAGTGCAGAAGGGCTGAGTCTTCAGTGGGTCAT
GCTGGAGCTAGTGACCTGGACTGGGACTATGGTTTACAGCATCACCAACAAGTTTCCCTTCGGCTCTTGGGGTGAAGCCC
TCTTCCTGATGATCCAGACGCTCACCATTGGCTGCCTGGTCCTGCACTACAGGAGGCAGACTGTGAAAGGAGCCGCTTTC
CTACTGTTACACCCTGCTCCTGTTGCTGCTGCTCTCACCCCTGACCTCGCTGGCCGTGGTCACTTGGCTCCAGGCTTCCA
GCGTGCCTGCTGTGGTAGGGGGCAGGCTGCTCCAGGACACCACCAACTACTACAATGGGCACACAAGTCAGCTCTCAGCC
ATCACGGTCTTTCTCTTGTTTGGGGGCTCTCGGGCCCGGATCTTCACCTCCATTCAGGAAACGGGAGACCCTCTCGTGGC
TGGCACC

Alignment

ORF - retro_etel_1794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTAEGGGALKRALVPLLLPEK-YDRLFVQWDLLHVPCLKILLSKGLGLGIVSASLLVKLPQVFKI-LSAK
          MTAE..G.LKRALVPLLLPEK.YDRLF.QWDLLHV.CL.ILLSKGLGLGIV..SLLVKLPQVFKI...AK
Retrocopy MTAEEHGVLKRALVPLLLPEKCYDRLFIQWDLLHVSCLQILLSKGLGLGIVFTSLLVKLPQVFKI>RAAK

Parental  SAEGLSLQSVMLELVALTGTMVYSTTNKFPFSSWGEALFLMLQTLTIGFLVLHYRGQTVKGVAFLVCY-T
          SAEGLSLQ.VMLELV..TGTMVYS.TNKFPF.SWGEALFLM.QTLTIG.LVLHYR.QTVKG.AFL.....
Retrocopy SAEGLSLQWVMLELVTWTGTMVYSITNKFPFGSWGEALFLMIQTLTIGCLVLHYRRQTVKGAAFLLLH>L

Parental  LLLLLLLSPLTPLAVVTWLQASNVPAVVGGRLLQATTNYYNGHTGQLSAITVFLLFGGSLARIFTSIQEK
          LLL.LLLSPLT.LAVVTWLQAS.VPAVVGGRLLQ.TTNYYNGHT.QLSAITVFLLFGGS.ARIFTSIQE.
Retrocopy LLL-LLLSPLTSLAVVTWLQASSVPAVVGGRLLQDTTNYYNGHTSQLSAITVFLLFGGSRARIFTSIQET

Parental  -EPFMAGT
          ..P..AGT
Retrocopy GDPLVAGT

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_1794 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000018609	3 retrocopies	retro_etel_1794 , retro_etel_2092, retro_etel_331,
Sus scrofa	ENSSSCG00000017955	1 retrocopy	retro_sscr_761,