RetrogeneDB ID: retro_etel_1923

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_314418:39321..39838(+)
• 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_1923
ATTGGTGGAAAATCACCAGATACAAATGACTAGTTTATGGGAGATTACGTGGACAGAGGCTATTATTCAGTTGAAACAGT
TACACTGCTTGCAGCTCTTAAGGTTTGTCACCCTGAACTCTCATCATTCTTCCAGGGAAGCATGAAAGCAGACAGATCAC
ACAAGTATGTGGTTTCTATGCTGAATGTTTATGGAAATGTGGGGACATATTTTACAGATCTCTTTGACTATCTTCCTCTC
ACTGCCTTGGTGGATGGGCAGACCTTTGTCTATGTGGCGGCCCCTCACCATCCATAGATACACCGGATCACATCAGGGCG
CTTGACCCCCTACAAGAAGTTCTTCAGGAGGGCCCAATGTGTGACCTACTGTGGTCACATCCAGATGACCGAGGAGGTTG
GGGGATATCTCCTCGAGGAGTTGATTACACCTTTGGACAAGATATTTCAGAGACATTTAATGATGCCAATGGCCTTACGG
GGGTGTCGAGAGCTCACAACTGGGAATGGAGGGATAT

Alignment

ORF - retro_etel_1923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 57.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNA
          IGGKSPDTN..FMGDYVDRGYYSVETVTLL.ALKV..PE......G...S.............L..YGN.
Retrocopy IGGKSPDTND*FMGDYVDRGYYSVETVTLLAALKVCHPELSSFFQG---SMKADRSHKYVVSMLNVYGN-

Parental  NVWKYFTDLFDYLPLTALVDGQIF-CLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGW
          .V..YFTDLFDYLPLTALVDGQ.F.CL.GG.SPSIDT.DHIRALD.LQEV..EGPMCDLLWS.PDDRGGW
Retrocopy -VGTYFTDLFDYLPLTALVDGQTF<CLCGGPSPSIDTPDHIRALDPLQEVLQEGPMCDLLWSHPDDRGGW

Parental  GISPRGAGYTFGQDISETFNHANGLTLVSRAH-QLVMEGY
          GISPRG..YTFGQDISETFN.ANGLT.VSRAH.QL.MEGY
Retrocopy GISPRGVDYTFGQDISETFNDANGLTGVSRAH<QLGMEGY

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_1923 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,