RetrogeneDB ID: retro_etel_1607

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_282589:42322..42907(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSETEG00000018123
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9300]

Sequence

>retro_etel_1607
ATTGACAAGAAGATGTTCACCAAGGAGCTAGACCAGTGGGTCAAGCAGCTTAACGAGTGTAAACAGCTGAACGAGAACCA
AGTATGGACCCTGTGTGAAAAGGCTAAGGAAATTTTAACAAAAGAATCAAATGTGCAAAAGGTCCATTGCCCTGTTACTG
TTTGTGGAGATGTTCACCGTCAATTCCATCCTCTTATGGAACTCTTCAGAATTGGTGGGAAATCACCAGTTACAAACTAT
CTATTCATGGGCGACTACATAAACATAGGTTATTATTCTGTGGAGACTGTGATGCTTCTTGTGGCATTAAAGGTGGGTTA
TCCAGAACACATTACAATATTAAGAGGAAACCACGAAAGCTGACAAATTACTCAAGTATATGGCATTTATGATGAATGTC
TATGAAAATATGGAAATGATAATGTTTGGAAATATTTTACAGACCTATTTGGTTATCTTCCACTTATAGCTTCAGTAGAT
GGACAGATACTTTGTCTCCATGGTGGCCTTTTTCCATCCATCGATACATGAGATCATATAAGAGCTCTGGATCAATTACA
AGAAGTTCCACATGAGGGTCCAATG

Alignment

ORF - retro_etel_1607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.15 %
• Parental protein coverage: 63.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDDKAFTKELDQWVEQLNECKQLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
          .D.K.FTKELDQWV.QLNECKQLNENQV.TLCEKAKEILTKESNVQ.V.CPVTVCGDVH.QFH.LMELFR
Retrocopy IDKKMFTKELDQWVKQLNECKQLNENQVWTLCEKAKEILTKESNVQKVHCPVTVCGDVHRQFHPLMELFR

Parental  IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNA
          IGGKSP.TNYLFMGDY...GYYSVETV.LLVALKV.YPE.ITILRGNHES.QITQVYG.YDECL.KYGN.
Retrocopy IGGKSPVTNYLFMGDYINIGYYSVETVMLLVALKVGYPEHITILRGNHES*QITQVYGIYDECL*KYGND

Parental  NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPM
          NVWKYFTDLF.YLPL.A.VDGQI.CLHGGL.PSIDT.DHIRALD.LQEVPHEGPM
Retrocopy NVWKYFTDLFGYLPLIASVDGQILCLHGGLFPSIDT*DHIRALDQLQEVPHEGPM

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_1607 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001615	1 retrocopy	retro_amel_663,
Bos taurus	ENSBTAG00000009245	3 retrocopies	retro_btau_1199, retro_btau_1750, retro_btau_704,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Echinops telfairi	ENSETEG00000007561	2 retrocopies	retro_etel_1233, retro_etel_659,
Echinops telfairi	ENSETEG00000018123	4 retrocopies	retro_etel_1607 , retro_etel_1923, retro_etel_680, retro_etel_702,
Felis catus	ENSFCAG00000025139	1 retrocopy	retro_fcat_1884,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,
Otolemur garnettii	ENSOGAG00000002488	1 retrocopy	retro_ogar_3188,
Tursiops truncatus	ENSTTRG00000000102	1 retrocopy	retro_ttru_1576,