RetrogeneDB ID: retro_etel_224

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_3834:55218..55661(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYSMD2
• Ensembl ID: ENSETEG00000020371
• Aliases: None
• Description: LysM, putative peptidoglycan-binding, domain containing 2 [Source:HGNC Symbol;Acc:28571]

Sequence

>retro_etel_224
GCGGGCGTCCCCCGAGCGCCCCTGGGGCACCGGGTCTGCTTGGGCGAAACGCTGCAGGGCATCGCGCTCAAGTACGGAGT
CACAGTGGTGCCGATAAAAAGAGCAAACAAACTATTTCCCAATGATTGTATATTTCTGAAGAAAACTGAGCATCCCAGTT
ATATTAGAGAAGCCTTTGTTGTTTAATGGACTTAACGGATCTCCAGCAAAGGAAACTAATAGCAGTCATTCTCCCGGAGA
GAAGCCGCAGGTGCCTGGGGCCCAACTGGCCCCTCCCAGTGGGCAGGAAGGGACGCGCAGCCCGTGCAGCCCAAGGAAGT
GCCAGCCTGGGATTTCCTGCAGAGACTAGACTTGCAGTTTAAGCTCTCAACACACGCAGCCAAGAAACTGAACGAAGACA
GCAGAGATGAGACGGTCCCTCTGCAACTTCTCTCTATCACAGT

Alignment

ORF - retro_etel_224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.81 %
• Parental protein coverage: 75.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AGAIERLVEHRVCSGCTLQGIALK--VKMEQIKRANKLFTNDCI-FLKKTLNIPVISEKPLLFNGLNSID
          AG.......HRVC.G.TLQGIALK..V....IKRANKLF.NDCI.F..K.L.IPVI.EKPLLFNGLN...
Retrocopy AGVPRAPLGHRVCLGETLQGIALKYGVTVVPIKRANKLFPNDCI>F*RK-LSIPVILEKPLLFNGLNG--

Parental  SPENETVDGSLSHGEEPQGTRADLSPPSPQEA-DAEPVQPEEVSAQDFLQRLDLQIKLSTQAAKKLKEES
          SP..ET...S.S.GE.PQ...A.L.PPS.QE..DA.PVQP.EV.A.DFLQRLDLQ.KLST.AAKKL.E.S
Retrocopy SPAKET-NSSHSPGEKPQVPGAQLAPPSGQEG<DAQPVQPKEVPAWDFLQRLDLQFKLSTHAAKKLNEDS

Parental  RDE-DSPYAASLYHS
          RDE.D.P.A.SLYHS
Retrocopy RDE<DGPSATSLYHS

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_224 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000020371	1 retrocopy	retro_etel_224 ,