RetrogeneDB ID: retro_etel_1704

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_288372:99186..99714(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APMAP
• Ensembl ID: ENSETEG00000015666
• Aliases: None
• Description: adipocyte plasma membrane associated protein [Source:HGNC Symbol;Acc:13238]

Sequence

>retro_etel_1704
GAATCCAGAGATGTGGAACCTGCCTGTGGGAGACTGCTGGGCATTCGGACAGGGCCCAGCAGGGGTATTTTTGTGGCTGA
TGCCTGCAAAGGACTATTTGAAGTAAATCCCTGGAAATACAAAGCAAAAACACTGTTGTCTTCTGAGACACCATTTTAGG
CGGGGAAATGTCCTTTGCTAATGATCTGGCAGTAACTCGGGATGGGAGGAAAATTCATCATACATATTCTAGCAGCAAAT
TGCAAAGCTGTGACGATCCGCTTTTGGTTATGGAGGGGCCAGATGACTGGGCATCTGCTAGAATTTGACACTGTGACCAA
GGAAGAATAAGTCTTAATGGACCACTTGCAATTCCCTAAAGGAGTTGAGTTTTCTCCAGAGGAGGACTTTTTCTTGGTGG
CAGAAATGACCATGGCAAGGATCAGAAGCTTCTATGTACCTGGTCTGATGAAGGGAGGGGGCAGATATGTTTGTGGAGAA
CATTCCTGGATTTCTGGACAACACATGCCCAGCAGCTCCAAGGGATAT

Alignment

ORF - retro_etel_1704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.89 %
• Parental protein coverage: 51.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KSRDDEPACGRLLGIRAGLNRTLFVADAYKGLFEVNLWKREVKILLSSETP-IEGKKMSFVNDLTITQDG
          .SRD.EPACGRLLGIR.G..R..FVADA.KGLFEVN.WK...K.LLSSETP.I.G..MSF.NDL..T.DG
Retrocopy ESRDVEPACGRLLGIRTGPSRGIFVADACKGLFEVNPWKYKAKTLLSSETP<ILGGEMSFANDLAVTRDG

Parental  RKIYFTDSSSKWQRRDYLLLVMEGTSD-GRLLEYDSGRKEVKVLMDQLQFPNGVQLSPAEDFVLVAETTM
          RKI..T.SSSK.Q..D..LLVMEG..D.G.LLE.D...KE..VLMD.LQFP.GV..SP.EDF.LVAE.TM
Retrocopy RKIHHTYSSSKLQSCDDPLLVMEGPDD>GHLLEFDTVTKEE*VLMDHLQFPKGVEFSPEEDFFLVAEMTM

Parental  AWIRRFYVSGLMKG-GADMFVENMPGFPDNI-RPSSSGGY
          A.IR.FYV.GLMKG.GADMFVEN.PGF.DN...PSSS.GY
Retrocopy ARIRSFYVPGLMKG>GADMFVENIPGFLDNT<MPSSSKGY

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_1704 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015666	1 retrocopy	retro_etel_1704 ,