RetrogeneDB ID: retro_etel_331

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_5421:111635..112096(-)
• 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_331
ATGGTGGCCAAGGCGGATAGGCCATAGAAATGGGTTCTAGTGCCAGTTCTTCTACCTGAGAAATGCTACCACTAAAGGTC
TGTCCAGTGGGACTTGCTTCACGTCCCTTGCCTCAAGATTCTTTTCAGCAAAACCCCAGGGCGAGGCATTTACCTAGGGC
AGTTCTGGTAAACCTGCCTCAGGTGTTTAAAATCCTGGGAGCCAACAATGCCGTAGGGCTGAGTCTCCAGCCAGTCATGC
TAGGGTCAGCGTCCTTGTCTGGGACCGTGGTCTACAGCATCACCAACAAGCTTCCCTTCATCTCTTGGGGTGAAACCTTG
TTCCTGATGCTTCAGATGACCGCCATCCGTGTCCTGGTCCTGCCCCTCGGAGGACAGGCTGTGAGAGGTGTTGCTTTGCT
GGCCTGCTGCACTCTGCTCCTCTTGGCGCTGCTCTCACCCCTGACATTTTTGCCTGTGGTG

Alignment

ORF - retro_etel_331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.23 %
• Parental protein coverage: 71.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTAEGGGALKRALVPLLLPEK-YDRLFVQWDLLHVPCLKILLSKGLGLGI-VSASLLVKLPQVFKILSAK
          M.A......K..LVP.LLPEK.Y....VQWDLLHVPCLKIL.SK..G.GI......LV.LPQVFKIL.A.
Retrocopy MVAKADRP*KWVLVPVLLPEKCYH*RSVQWDLLHVPCLKILFSKTPGRGI<LPRAVLVNLPQVFKILGAN

Parental  SAEGLSLQSVMLELVALTGTMVYSTTNKFPFSSWGEALFLMLQTLTIGFLVLHYRGQTVKGVAFLVCYTL
          .A.GLSLQ.VML....L.GT.VYS.TNK.PF.SWGE.LFLMLQ...I..LVL...GQ.V.GVA.L.C.TL
Retrocopy NAVGLSLQPVMLGSASLSGTVVYSITNKLPFISWGETLFLMLQMTAIRVLVLPLGGQAVRGVALLACCTL

Parental  LLLLLLSPLTPLAVV
          LLL.LLSPLT.L.VV
Retrocopy LLLALLSPLTFLPVV

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_331 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,