RetrogeneDB ID: retro_etel_1946

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_318654:37825..38841(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSETEG00000004811
• Aliases: None
• Description: SDA1 domain containing 1 [Source:HGNC Symbol;Acc:25537]

Sequence

>retro_etel_1946
CTCTTACTGAGAAACAAGAATCTTATCAACTCATCGAGTTTCCTAGAGCTCTTCGTGGAACTTCTGTGTTTCTATGAGAA
GCTTCTGAAAAGAATTTATACACTCACATTGTGACCGAGGGCAAGAACACAAAACAAACACAAGAACAATAAAGTACCTG
TAGTGCTGCAAAATTTTACACAATGCTAAGACACAGTAATAAAACTACATCTAAGATCTCTTGGAATGGGATGATTGAAC
TCCACAAAGAAAACATTTGGAATTATGCCCAAACTGTCCATGTTACCACAACTCTATGTTTCTCCAAGGTCACTAATTTA
TTAGTGACTGCTTCGGCATTCTTCAAACAGGAGAAGCAGCGCAACTACTTGAATTCGAAGACATAAGGATCAACATCGAG
AAACCTCCTAGTGCAGTATGCCACTGGGAAGGAAAGCTCCAAAGCCAAGGTGAAGACTGGAGAAGGCTATGAAAGTGCCC
AAGATACAAAAGAAGAAATAAAGGGGAGTGTTGGACTTTTCAGCCATTCTCTCGCTTCCTGATCCCCAAGATTTTTCAGA
AAAACAACTAAAAACGTATAGAGCTCCAAAGAGAACTTTGAAGTGAAGATGATGCTCAGGACCCTTATCTCCAGATTCCT
GGGAATTCTTGTGCTTTTCTTCTTTAACTTCCATCCCTTTGTTCAAAACTTCTTTCAGCCCCACCAAAGTACCAAACATC
CTTCTGTTTACTGCACACGCTTTTCATCACCTGGTGACCCCAGAGTTCATGCCATCATTGCTGATGACTGTGGCCAACAA
TTTCGTCACTGGATAGAACTCTAGCGAAGTTAAGACCTTAGGAATCAAGGCTATGGAAGAAATAACAGCTCGATGGCCCC
TACCCATGACTGAAGGACTTCTCCAAGACCTGGCTCAGGAGAAAACACACAAAGATAAGAAGGTGCAATGTCAGCAGGAA
CTTTGATTCAGCTCTTCCGACCACGGAGTCTTCAGATGTTGTACACGGAATTCCAG

Alignment

ORF - retro_etel_1946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.09 %
• Parental protein coverage: 55.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ILLRNKNLINPSSLLELFFELLRCHDKLLR-KTLYTHIVTDIKNINAKHKNNKVNVVLQNFMYTMLRDSS
          .LLRNKNLIN.SS.LELF.ELL....KLL..K.LYTHIVT..K..N.K..............YTMLR.S.
Retrocopy LLLRNKNLINSSSFLELFVELLCFYEKLLK<KNLYTHIVTEGK--NTKQTQEQ*STCSAAKFYTMLRHSN

Parental  ATAAKISLDVMIELYRRNIWNDAKTVNVITTACFSPVTKILVAALTFFLKDEQEKQDSDSDSEE-GPTAR
          .T..KIS...MIEL...NIWN.A.TV.V.TT.CFS.VT..LV.A..FF....QEKQ.....S...G.T.R
Retrocopy KTTSKISWNGMIELHKENIWNYAQTVHVTTTLCFSKVTNLLVTASAFF---KQEKQRNYLNSKT*GSTSR

Parental  DL-VQYATGKKSSKHKKK-LEKAMKVLKKQKKKKKPEVFNFSAIHLIHDPQDFAEKLLKQLE-SSKERFE
          .L.VQYATGK.SSK.K.K.LEKAMKV.K.QKKK....V..FSAI....DPQDF.EK.LK....SSKE.FE
Retrocopy NLLVQYATGKESSKAKVK>LEKAMKVPKIQKKK*RG-VLDFSAILSLPDPQDFSEKQLKTYR<SSKENFE

Parental  VKMMLMNLISRLVGIHELFLFNFY-PFVQRFLQPHQREVTKILLFAAQASHHLVPPEIIQSLLMTVANNF
          VKMML..LISR..GI..LF.FNF..P.......P....V..ILLF.A.A.HHLV.PE...SLLMTVANNF
Retrocopy VKMMLRTLISRFLGILVLFFFNFH>PLFKTSFSP--TKVPNILLFTAHAFHHLVTPEFMPSLLMTVANNF

Parental  VTDKNSGEVMTVGINAIKEITARCPLAMTEELLQDLAQYKTHKDKNVM-MSARTLIQLFRTLNPQMLHKK
          VT..NS.EV.T.GI.A..EITAR.PL.MTE.LLQDLAQ.KTHKDK.V..MSA.TLIQLFR....QML...
Retrocopy VTG*NSSEVKTLGIKAMEEITARWPLPMTEGLLQDLAQEKTHKDKKVQ<MSAGTLIQLFRPRSLQMLYTE

Parental  FR
          F.
Retrocopy FQ

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_1946 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008521	2 retrocopies	retro_cfam_1211, retro_cfam_515,
Echinops telfairi	ENSETEG00000004811	2 retrocopies	retro_etel_1946 , retro_etel_779,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Microcebus murinus	ENSMICG00000006682	1 retrocopy	retro_mmur_1204,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Sus scrofa	ENSSSCG00000008974	1 retrocopy	retro_sscr_571,