RetrogeneDB ID: retro_etel_2115

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_65168:422..942(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: B9D1
• Ensembl ID: ENSETEG00000001144
• Aliases: None
• Description: B9 protein domain 1 [Source:HGNC Symbol;Acc:24123]

Sequence

>retro_etel_2115
TCAGTGATTCCTAGCGTCTTCCTACTATGGTCAGCGGGCAGGTGGAGAGTGCCCAGGTTCCAGAATAGGATGACCTCCAC
TGCTAGGACTGCCTTGTGGCTGGGCAGGCCTGGGCTCCTTCAGCGGGTTTGGAGGAGGACATCTCACAGATGACATCCAA
GAGTCAAGCTATGCAGCGACTGCTCACACAGTACTTTCCCATTGATGGTACCTTTAAAGGCACCAACCCCTTTGGCTGGC
CACAGATCCTGCTCAGTGTGTATGGACCGGATGTATTTGGGAATGATGTGGTCTGAGGCTATGGGGTGGTGCATGTACCT
TGCTCACCTGGCTGACACAAAATGACCATAGTGTTTGTCCCTGAATCTACATCTAAGGTGCAAAAGTTTACAAGCTGGTT
CACGGGACGGTGGCCTGAGTACACAGACCCCAAGGTGGTGACTCAGGGTGAAGGCCAGGAGGTGACTCTAATCTGCTCCC
AGGGTTTCATCTCCCCTCCTCTTTCAACATTGTCACCAAA

Alignment

ORF - retro_etel_2115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.14 %
• Parental protein coverage: 85.29 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVVPSVFLL-MVNGQVESAQFPEYDDLYCKYCFVYGQDWAPTAGLEEGISQITSKSQDTRQLLTWNFPID
          SV.PSVFLL.MV.GQVESAQ.PE.DDL.C..C.V.GQ.WAP.AGLEE.ISQ.TSKSQ....LLT..FPID
Retrocopy SVIPSVFLL<MVSGQVESAQVPE*DDLHC*DCLVAGQAWAPSAGLEEDISQMTSKSQAMQRLLTQYFPID

Parental  VTFKSTNLSGWPQIVLSVYGPDLFGNDVVRGYGVVHIPFSPGRHKRTIPMFVPESTSKVQKFTSWFMGRR
          .TFK.TN..GWPQI.LSVYGPD.FGNDVV.GYGVVH.P.SPG.HK.TI..FVPESTSKVQKFTSWF.GR.
Retrocopy GTFKGTNPFGWPQILLSVYGPDVFGNDVV*GYGVVHVPCSPG*HKMTI-VFVPESTSKVQKFTSWFTGRW

Parental  PEYTDPKVVAQGEGREVTRVRSQGFIT-LLF-NVVTK
          PEYTDPKVV.QGEG.EVT...SQGFI..LLF.N.VTK
Retrocopy PEYTDPKVVTQGEGQEVTLICSQGFIS>LLF>NIVTK

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_2115 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000001144	3 retrocopies	retro_etel_1347, retro_etel_149, retro_etel_2115 ,