RetrogeneDB ID: retro_sara_385

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_189393:278..1086(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSSARG00000005447
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9299]

Sequence

>retro_sara_385
AAAGAAATCCTGACAAAAGAATCCAACGTGCAAGAGGTTCGATGTCCAGTTACCATCTGTGAAGATGTGCAGGGGCAATT
TCATGATCTCATGGAATTGTTTAGAATTGGTGGCAAATCACCAGAAACAAATTACTTGTTTATGGGAGATTATGTTGACA
GAGGATATTACTCAGTTGAAACAGTTACTCTACTACAAGCTCTTAAGGTTCGTTACTGTGAGCGCATTTCTATTCTTTGA
GGAAATCATGAGAGCAGACAGATCACACAAGTATATGGTTTCTATGATGAGTGCTTAAGGAAATATGGAAATGCAAATGT
TTGGAAATACTTTACAGATCTTTTTGACTATCTTCCTCTCACTGCCTTGGTGGATAAGGCAGATCTTCTGTCTACATGGT
GGCCTCTCACCATCTACAGATACACTGGATTACATCAGAGCACTTGACCGCCTACAAGAAGTTTCCCATGAGGGTCCCAT
GTGTGACTTGCTGTGGTCAGATCCAGATGACCGTGGTGGTTGGGATATATCTCCCCTGGGAGCTTGTTACACCTTCAGGC
AAGATATTTCTGAGACATTCAATCATGCCAATGGCCTCACGCTGGTGTCTAGAGCCCACCAACTGGTGATGGAGGGATAT
AACTGGTGCCATGACCGGAACGTAGTAACGTTTTTCAGTGCCCCAAACTATTGTTATCATTGTGGTAACCAAGCTGCAAT
CATGGAAATTGATGATACTCTAAAATACTCTTTCTTGCAGTTTGACCCAGCAACTTGAAGTGGCGAGCCACATGTTACTC
ATTGTACC

Alignment

ORF - retro_sara_385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.74 %
• Parental protein coverage: 87.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKV
          KEILTKESNVQEVRCPVT.C.DV.GQFHDLMELFRIGGKSP.TNYLFMGDYVDRGYYSVETVTLL.ALKV
Retrocopy KEILTKESNVQEVRCPVTICEDVQGQFHDLMELFRIGGKSPETNYLFMGDYVDRGYYSVETVTLLQALKV

Parental  RYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDG-QIFCLHGGLSPSI
          RY.ERI.IL.GNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVD..QIFCLHGGLSPS.
Retrocopy RYCERISIL*GNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDK>QIFCLHGGLSPST

Parental  DTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLV
          DTLD.IRALDRLQEV.HEGPMCDLLWSDPDDRGGW.ISP.GA.YTF.QDISETFNHANGLTLVSRAHQLV
Retrocopy DTLDYIRALDRLQEVSHEGPMCDLLWSDPDDRGGWDISPLGACYTFRQDISETFNHANGLTLVSRAHQLV

Parental  MEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTRRT
          MEGYNWCHDRNVVT.FSAPNYCY.CGNQAAIME.DDTLKYSFLQFDPA...GEPHVT..T
Retrocopy MEGYNWCHDRNVVTFFSAPNYCYHCGNQAAIMEIDDTLKYSFLQFDPAT*SGEPHVTHCT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_385 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus 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 17 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,
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,