RetrogeneDB ID: retro_etel_488

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_8044:182689..183525(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000008468
• Aliases: None
• Description: None

Sequence

>retro_etel_488
TACAGTATGGTGCTCTCCATGGAAATTGACATTCACCATGGAGACCGCATGGAAGAGGCCTTCTGCACCACAGACCGGGT
CATGACCGTGTCCTTCCACCAGTATGGGGAGTACTTCCCAGGGACCGGGGACTTGCGGGACCATTGGCGCTGACAAAGGC
CAAGTATTATGCTGTCAACTACCCGCTCGAGATGGGATTGACGACAAGTCTACGAAGCCGTTGTCAGACCAGTCATCTCC
AAGATCATGGAGATGTTCCAGCCGAGCGCGGTTGTCCTCCAGTGTAGCTCCGACTCCTTGTCTGGGGATTGGCTAGGTTG
TTTGAACCTGACCATCAAAGGGCACGCCAAGTGTGTAGAATTTGTGAGGCATTTCAACCTGCCGATGCTGATGCTGGGAG
GAGGTGGTTACACCATTCGCAGTGTCACGCGGCGCTGGACATATGAGACAGCTGTGGCCTGGAGCACAGAGATCCCCAAT
GAGCTTCCATCCAACGACTCCTTTGAATACTTCACACCAGATTTCAAGCTTCACCTCAGCCCTTTCAACATGCCCAACCT
GAACACTAATGAGTACCTGGAGAAGATCAAGCAGAGACTCTTTGAGAAGCTGAGGATGTTGCCCCACACCCTTGAGATCC
AGATGCAAGTGATCCTGAGGACACCGTCCCAGAGGAAAGTGGCAATGAGGAGTAAGAGGACCCCGAGAAGCACATCTCAA
TCTGCTCCTCTGGCAAGCGAATTGCTTGGGAAGAAGAGTTCTCTGACTCTGATGAAGAGGGAGAGGGTGGCCGCAAAAAC
TCTTCCAACTTCAAAAAAGACGAGAGTCAACATAGA

Alignment

ORF - retro_etel_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.13 %
• Parental protein coverage: 57.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRD-IGAGKG-KYYAVNFPM-RDGID
          ...VL...IDIHHGD..EEAF.TTDRVMTVSFH.YGEYFPGTGDLRD.IGA.KG.KYYAVN.P..RDGID
Retrocopy YSMVLSMEIDIHHGDRMEEAFCTTDRVMTVSFHQYGEYFPGTGDLRD>IGADKG>KYYAVNYPL<RDGID

Parental  DES-YGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGG
          D.S.Y.....P.ISK.MEM.QPSAVVLQC..DSLSGD.LGC.NLT.KGHAKCVE.V..FNLP.LMLGGGG
Retrocopy DKS<YEAVVRPVISKIMEMFQPSAVVLQCSSDSLSGDWLGCLNLTIKGHAKCVEFVRHFNLPMLMLGGGG

Parental  YTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRM
          YTIR.V.R.WTYETAVA...EIPNELP.ND.FEYF.PDFKLH.SP.NM.N.NT.EY.EKIKQRLFE.LRM
Retrocopy YTIRSVTRRWTYETAVAWSTEIPNELPSNDSFEYFTPDFKLHLSPFNMPNLNTNEYLEKIKQRLFEKLRM

Parental  LPHAPGVQMQAI-PEDAVHEDSGDEDGEDPDKRISIRASDKRIASDEEFSDSEDEGEGGRRNVADHKKGA
          LPH....QMQ.I.PED.V.E.SG.E..EDP.K.ISI..S.KRIA..EEFSDS..EGEGGR.N....KK..
Retrocopy LPHTLEIQMQVI<PEDTVPEESGNEE*EDPEKHISICSSGKRIAWEEEFSDSDEEGEGGRKNSSNFKKDE

Parental  KKAR
          ...R
Retrocopy SQHR

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_488 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Echinops telfairi	ENSETEG00000008468	1 retrocopy	retro_etel_488 ,
Myotis lucifugus	ENSMLUG00000003117	4 retrocopies	retro_mluc_1570, retro_mluc_225, retro_mluc_2548, retro_mluc_935,
Monodelphis domestica	ENSMODG00000017860	1 retrocopy	retro_mdom_597,
Ornithorhynchus anatinus	ENSOANG00000003631	1 retrocopy	retro_oana_79,
Pan troglodytes	ENSPTRG00000018519	1 retrocopy	retro_ptro_69,
Sorex araneus	ENSSARG00000000354	1 retrocopy	retro_sara_651,
Ictidomys tridecemlineatus	ENSSTOG00000012779	1 retrocopy	retro_itri_374,
Tarsius syrichta	ENSTSYG00000009363	4 retrocopies	retro_tsyr_1337, retro_tsyr_1355, retro_tsyr_681, retro_tsyr_765,
Tursiops truncatus	ENSTTRG00000015043	1 retrocopy	retro_ttru_462,