RetrogeneDB ID: retro_etel_659

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_134232:230..1031(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000001579
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSETEG00000007561
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9299]

Sequence

>retro_etel_659
ATCCTGACAACAGACTCCAACGTGCAAGAAGTGGGATGTCCAGTCACTGTCTGTGGAGATGTGCATCGCCAATGTCAGGA
TCTCGTGCAACCGCTTAGAAGTGAGGGCAAATCACCAGGTACAAATCACCTGTTTATGGGAGATCACGGTGACAGAGGCT
ATTATTCAGTTGAAACAGTTACACTGCTTGTAGCTCTTTAGGATCGTTACCGTGAACGCATCACCATTCTTCGAGGAAAT
CATGAGAGCGGACAGAGCATCACACAAGTATATGGTTTCCTATGATGAATGTTTAAGGGAATATGGAAATGCAAATGTGT
GGAAATATTTTACAGATCTTTTTGACTATCTTCCTCTCACTGCCTTGGTGGATGGGCAGATCTTCTGTCTACATGGTGGC
CTCTCACCGTCCATTGATACCCTGGATCACATCAGAGCGTTTGACTGCCTACAAGAAGTTCCTCATGAGGCCCAACGTGT
GACTTGCTGTGGTCATCCAGATGACCGAGGTGGTAGGGGATATCTCCTTGAGGAGCGGGCTACACCTTTGGACAAGATAT
TTCTGAGACATTTAATCATGCCAATGGCCTTACGTTGATGTCGAGAGCTCACCAACTGGTAATGGAGGGATATAACTGAT
GCCATGACCAGAATGTAGTAACAATTTTCAGTGCTCCAAACTATTGCTATCGCTGTGGCAACCAAGCTGCAATCATGGAA
CTTGACAATACTCTAAAATACTCTTTCTTCCAGTTTGACCCGGCACCACGCAGAGGTGAGCCACATGTCACTCGTCGCAC
C

Alignment

ORF - retro_etel_659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.44 %
• Parental protein coverage: 86.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ILTKESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRY
          ILT..SNVQEV.CPVTVCGDVH.Q..DL....R..GKSP.TN.LFMGD..DRGYYSVETVTLLVAL..RY
Retrocopy ILTTDSNVQEVGCPVTVCGDVHRQCQDLVQPLRSEGKSPGTNHLFMGDHGDRGYYSVETVTLLVAL*DRY

Parental  RERITILRGNHESRQ-ITQVYGF-YDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSID
          RERITILRGNHES.Q.ITQVYGF.YDECLR.YGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSID
Retrocopy RERITILRGNHESGQSITQVYGF>YDECLREYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSID

Parental  TLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWG-ISPRGAGYTFGQDISETFNHANGLTLVSRAHQLV
          TLDHIRA.D.LQEVPHE..........PDDRGG.G.ISP.GAGYTFGQDISETFNHANGLTL.SRAHQLV
Retrocopy TLDHIRAFDCLQEVPHEAQRVTCC-GHPDDRGGRG<ISP*GAGYTFGQDISETFNHANGLTLMSRAHQLV

Parental  MEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTRRT
          MEGYN.CHD.NVVTIFSAPNYCYRCGNQAAIMELD.TLKYSF.QFDPAPRRGEPHVTRRT
Retrocopy MEGYN*CHDQNVVTIFSAPNYCYRCGNQAAIMELDNTLKYSFFQFDPAPRRGEPHVTRRT

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_659 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Bos taurus	ENSBTAG00000000469	1 retrocopy	retro_btau_1754,
Dasypus novemcinctus	ENSDNOG00000013011	4 retrocopies	retro_dnov_1025, retro_dnov_1844, retro_dnov_2100, retro_dnov_2122,
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	ENSFCAG00000029685	1 retrocopy	retro_fcat_1086,
Mustela putorius furo	ENSMPUG00000010169	1 retrocopy	retro_mputfur_633,
Sorex araneus	ENSSARG00000005447	3 retrocopies	retro_sara_296, retro_sara_385, retro_sara_715,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Tursiops truncatus	ENSTTRG00000016859	1 retrocopy	retro_ttru_1584,