RetrogeneDB ID: retro_etel_352

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_5836:150209..150822(+)
• Located in intron of: ENSETEG00000008569

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000009155
• Aliases: None
• Description: None

Sequence

>retro_etel_352
GAAGAACCATTCTGTACTTGCAAGCTTTGGTTCACTGCTCTTCGACCTGAATTGGTGCCGTCAGCTCTGGAGAAGTCACT
GCAAAAACTCCAGCTATCTTCGTTGATCTCTACCTGATTCCCTGGGCGGGGCCTCTAAAGCCTGGAGAGATTTTCCCACA
AGATGAACATGGAAAACTAGCATTTGGTACAGAGGCTCTCTGTGCCACATGGGAGGCCCTGTAGAAGTGTAAGGATGTAC
GATTGACCAAGTCCATTGGCGAGTCCAGCTTTAGCCACAAGCAGCTAAAGATAATTCTGAACAAGCCAGGGCTCAAATAC
GAACCTGTCTGCAATCAGGTAGAATGTCACCCTTACATCAACCAGAGCAAACTGCTGGGTTTCTGCAAGTCTAAAGAGAC
TGTTTGGGTTGCCTATGGTGTTCTGGGAACCCAACGGTAGAAGCTATGTGTAGCCCAGAGCTCCCCTGTTCTCTTAGATG
ATCCAGTTCTTGGTACCTTGGCAAAAAAGTACGAAAGAACCCAGCCCAAGTTGCCCTTCGATACTAGATCCACCGGGGGA
TCGTGGACCTGGCCAAGAGTCACAGTGAGCCGAGGCTCGAAGAGCACACACAG

Alignment

ORF - retro_etel_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.35 %
• Parental protein coverage: 81.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDIFYTSKLWVTFLRPELAQSALEISLKKLQLD-YVDLYLIHYPTALKPGEEMIPEDEHGKVIFDTVDFC
          E..F.T.KLW.T.LRPEL..SALE.SL.KLQL...VDLYLI.....LKPGE...P.DEHGK..F.T...C
Retrocopy EEPFCTCKLWFTALRPELVPSALEKSLQKLQLS<FVDLYLIPWAGPLKPGE-IFPQDEHGKLAFGTEALC

Parental  ATWEVLEKCKDDGLAKSIGVSNFNHKQLEMILNKPGLKYKPVCNQVECHPYLNQSKLLDFCKSKDIVLIA
          ATWE.L.KCKD..L.KSIG.S.F.HKQL..ILNKPGLKY.PVCNQVECHPY.NQSKLL.FCKSK..V..A
Retrocopy ATWEAL*KCKDVRLTKSIGESSFSHKQLKIILNKPGLKYEPVCNQVECHPYINQSKLLGFCKSKETVWVA

Parental  YGALGTQRDK-CVDQSSPVLLNDPVLGALAKKY-NQSPALIALRYQIQRGVVVLAMSFTEREIKENIQ
          YG.LGTQR.K.CV.QSSPVLL.DPVLG.LAKKY....PA..ALRY.I.RG.V.LA.S..E....E..Q
Retrocopy YGVLGTQR*KLCVAQSSPVLLDDPVLGTLAKKY<RKNPAQVALRY*IHRGIVDLAKSHSEPRLEEHTQ

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_352 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008668	1 retrocopy	retro_chof_568,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Echinops telfairi	ENSETEG00000006450	1 retrocopy	retro_etel_1106,
Echinops telfairi	ENSETEG00000009155	1 retrocopy	retro_etel_352 ,
Rattus norvegicus	ENSRNOG00000038361	1 retrocopy	retro_rnor_2046,
Sarcophilus harrisii	ENSSHAG00000006005	1 retrocopy	retro_shar_520,