RetrogeneDB ID: retro_etel_1208

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_227840:11242..12355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOM1L1
• Ensembl ID: ENSETEG00000017657
• Aliases: None
• Description: target of myb1 (chicken)-like 1 [Source:HGNC Symbol;Acc:11983]

Sequence

>retro_etel_1208
GTTCAGACTGAAGACTGGGGCCAGTTCATGCACGTCTGTGACGTCATCAACACCTCCCAAGATGGACCAAAGGATGCAGT
AAAAACTTTGAAGAAAGGGATTTCCAAAAACTACAACCATAAAGAAATCCAACGTACGTACTTTGTCACTTATTGACATG
TGCATGCAGAATTGTGGACCAAGTTCCCAACCTCTGATCGTAAAGAAGGAGTTTGTGAAAGATTGTCTAGTAAAGCTGCT
GGGATCCCAGATACAACTTGCCCTTAGACCCTCAGAATGAACTCTTGAATTTCATGAAAACGTGGTCATAGTGCTTCCCG
GGAGGTGTGGATGTAAGTGAAGTGAAGGAAGTGTATCCTGACCTGCTTATGAAAGGTGTGCAGCTTCTCCTTCCGATGCA
GAGGTGGAAACAACACGACCAGAGACTGCTCCCATCAGGTCGAATCCACCCAACATCTGTTCCTAGGCACTGGCCCTTCC
TTCTGCAGTGGTCCCCAAGAACTCAACCCTTATGTTGGCCCCAGAACAGATTGGAAAACCACACAGTGAGGTAGACATGG
GGACAATGAATGTGAGTGTGATGTTCACCACATAACTGGAGATTACCCCCAGGTCTGAAAACCATGAAGACGTACAGCTT
CTTTAGGAACTTTATAAGATGTGTGGAAAGATACAGGAGAGGATCATGGACCTACTGGCAGTAGTGGAGAATGAAAATAT
AACTATTGAGCAAAGTAAAGCAAATGAGGATTTGAATAATGCCCTCCTTGGATACGAGAGATTCACTCGGAACCAACAAA
GGATGTGGGAGCAAAATGAGAACCAGGAGGAAGCTGCCAATACTGCCAGTGGACCTTCTGCCCCATCTTGTGATCTCCTG
AACCTTAGCCCGAGTCATCCGACTCCTAAGGCCCCTCTGAGAGAATTCAACATCATCAATGCTCCGCTTTCAGACTTAAG
TGTTCGATCTCCAAGTCCTGTCCTGTTGTAACAAACAACGTGAACCCCCCAGTCATCAGCCACAGGTGGATTTGCTAGCC
TCGGAAACCCCAGAAACACCCTTTCCCCCAAAGGACAGGCCAAAACCTTGCTTCAGGTCTTCCATCTGACAAT

Alignment

ORF - retro_etel_1208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.82 %
• Parental protein coverage: 80.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VQTEDWGQFMHICDVINTSQDGPKDAVKAL-KKRISKNYNHKEIQL-TLSLIDMCMQNCGPSFQSLIAKK
          VQTEDWGQFMH.CDVINTSQDGPKDAVK.L..K...K....K.....TLSLIDMCMQNCGPS.Q.LI.KK
Retrocopy VQTEDWGQFMHVCDVINTSQDGPKDAVKTL>RKGFPKTTTIKKSNVRTLSLIDMCMQNCGPSSQPLIVKK

Parental  EFVKDCLVKLL-NPKYNLPLDTQNKILNFIKTWSQGFPGGVDVSEVKEVYLDLLKRGVQF-PPSDAEAET
          EFVKDCLVKLL..P.YNLPLD.QN..LNF.KTWS..FPGGVDVSEVKEVY.DLL..GVQ...PSDAE.ET
Retrocopy EFVKDCLVKLL>DPRYNLPLDPQNELLNFMKTWS*CFPGGVDVSEVKEVYPDLLMKGVQL<SPSDAEVET

Parental  TRPETAPIPSNPPTSVPTAPALPSVVAPKNSTITLVAEQIGKLHSELDMVKMILSVMFTILLEITPGSEN
          TRPETAPI.SNPP.....A.ALPS.V.PKNST..L..EQIGK.HSE.DM..M..SVMFT..LEITP.SEN
Retrocopy TRPETAPIRSNPPNICS*ALALPSAVVPKNSTLMLAPEQIGKPHSEVDMGTMNVSVMFTT*LEITPRSEN

Parental  QEDVQLLQELYKTCREMQERIMDLLAVVENEDVTVELIKVNEDLNNALLGYERFTRNQQRIVEQNENQE-
          .EDVQLL.ELYK.C...QERIMDLLAVVENE..T.E..K.NEDLNNALLGYERFTRNQQR..EQNENQE.
Retrocopy HEDVQLL*ELYKMCGKIQERIMDLLAVVENENITIEQSKANEDLNNALLGYERFTRNQQRMWEQNENQEE

Parental  AANTASGPSAPSCDLLDLTSSHPTPEGPRGELNTVNAQLSDLSFR--SPT-PVLTNNMN-PSRHPQVDLL
          AANTASGPSAPSCDLL.L..SHPTP..P..E.N..NA.LSDLS.R..SP..PV.TNN.N.P..H.....L
Retrocopy AANTASGPSAPSCDLLNLSPSHPTPKAPLREFNIINAPLSDLSVRSPSPV<PVVTNNVN<PPSHQPQVDL

Parental  ASENTETPLFP-QRTGQNLASGHTYDN
          ....T....FP.QRTGQNLASG...DN
Retrocopy LASETPETPFP>QRTGQNLASGLPSDN

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_1208 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000017657	1 retrocopy	retro_etel_1208 ,
Oryctolagus cuniculus	ENSOCUG00000008462	1 retrocopy	retro_ocun_1187,