RetrogeneDB ID: retro_etel_2092

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_53357:2700..3277(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000008061
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2092
AGACTTTTCGTCCACTGGGACCTGCTGCACATCCCTTGCCTCAAGATTCTCCTCAGCAAAGGCCTGGGGCTGGGCCTTGT
ATCTAGCTCCCTGCTATTAAAACCGCCCCTGGTGTTTAAAATCCTGGGCGCCAAGAATGCAGACAGGCTGAGTCTTCAGT
GGGTCATGCTGGAGCTACTGACCTTGACTGGGACTATGGTCTACAGCATCACCAACAAGCTTCCCTTTGGCTCTTGGGGT
GAAGCCCTCTTCCTGATGCTCCAGACGCTCACCACTGGCTGCCTGGTCCTGCACTGCAGGGGCAGACTGTGAAAGGAGCT
GCTTTCCTAGTCGGTTCCACCCTGCTCCTGTTGCTGCTGCTCTCACCCCTGACCCCGCTGGCGTGGTCACTTGGCTCCAG
GCTTCCAGCGTGCCTGCTGTGGTAGGGGGCAGGCTGCTCCAGGCCACCACCAACGACTACAACAACGGGCACACAGGTCA
GCTCTTGGCCGCCACAGTCTTTCTCTTGTTTGGGGGCTCCCTGGCCCAGATCTTCAACCCCATTTAGGAAATGGGAGACC
CTCTCGTGGCTGGCACC

Alignment

ORF - retro_etel_2092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 89.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLFVQWDLLHVPCLKILLSKGLGLGIVSASLLVKLPQVFKILSAKSAEGLSLQSVMLELVALTGTMVYST
          RLFV.WDLLH.PCLKILLSKGLGLG.VS.SLL.K.P.VFKIL.AK.A..LSLQ.VMLEL..LTGTMVYS.
Retrocopy RLFVHWDLLHIPCLKILLSKGLGLGLVSSSLLLKPPLVFKILGAKNADRLSLQWVMLELLTLTGTMVYSI

Parental  TNKFPFSSWGEALFLMLQTLTIGFLVLHYR-GQTVKGVAFLVCYTLLLLLLLSPLTPLA-VVTWLQASNV
          TNK.PF.SWGEALFLMLQTLT.G.LVLH.R.GQTVKG.AFLV..TLLLLLLLSPLTPLA.VVTWLQAS.V
Retrocopy TNKLPFGSWGEALFLMLQTLTTGCLVLHCR<GQTVKGAAFLVGSTLLLLLLLSPLTPLA<VVTWLQASSV

Parental  PAVVGGRLLQATTN-YYNGHTGQLSAITVFLLFGGSLARIFTSIQEK-EPFMAGT
          PAVVGGRLLQATTN.Y.NGHTGQL.A.TVFLLFGGSLA.IF..I.E...P..AGT
Retrocopy PAVVGGRLLQATTNDYNNGHTGQLLAATVFLLFGGSLAQIFNPI*EMGDPLVAGT

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_2092 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,