RetrogeneDB ID: retro_sara_707

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_261318:107588..108226(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CB
• Ensembl ID: ENSSARG00000011890
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9282]

Sequence

>retro_sara_707
GATATCCACGGGAAGTATTGTGATTTGCTTTGCCTTTTTGAGTATGGTTGTTTCCCTTCAGAAAGCCACTACCTGTTTCT
TGGGGCCTATGTGGCCAGGGGGAAGCAGTCATTGGAGACTATCTGCCTCTCACTGACTTACAAAATCAAATATCCTAAGA
ATTTTTTTTCTTCTCAGAGGGAACCAGGAGTGTGCCAGCATCAATAGGATTTACGGATCTTATGACGAATGTAAAAGAAG
ATATAACATTAAACTATGGAAAACTTTCACAGATTGCTTTAACTGTTAACCAATAGCCGCCATCGTGGATGAGAAGATAT
TCTGCTGTCATGGAGGTTTATCACCAGATCTTCAATCTATGGAGCAGATATGGTGAATTATGCGACCAACTGATGTACCA
GATCAAGGCCTTCTTTGTGATCTTTGTCATCTGACCCCAATAAAGATGTCTTAGGCTGGGGTAAAAATGAAAGAGGAGTG
TCCTTCACATTTGGTGCATAAGTGATTGCAAAATTTCTCCATAAGCATGATTCGAATCTTATATGTAAAGCCCATCAGGT
GGTTGAAGATGGATATGAATTTTTTGCCAGAGGCAGTTTGTCACTCTATTTTCCACATCCAATTATTGTGGAGAGTTT

Alignment

ORF - retro_sara_707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.09 %
• Parental protein coverage: 92.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DIYGQYTDLLRLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFF-LLRGNHECASINR
          DI.G.Y.DLL.LFEYG.FP.E..YLFLG.YV.RGKQSLETICL.L.YKIKYP.....LLRGN.ECASINR
Retrocopy DIHGKYCDLLCLFEYGCFPSESHYLFLGAYVARGKQSLETICLSLTYKIKYPKXXX>LLRGNQECASINR

Parental  IYGFYDECKRRFNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGLLC
          IYG.YDECKRR.NIKLWKTFTDCFNC.PIAAIVDEKIFCCHGGLSPDLQSMEQI..IMRPTDVPD.GLLC
Retrocopy IYGSYDECKRRYNIKLWKTFTDCFNC*PIAAIVDEKIFCCHGGLSPDLQSMEQIW*IMRPTDVPDQGLLC

Parental  DL-LWSDPDKDVQGWGENDRGVSFTFGADVVSKFLNRHDLDLICRAHQVVEDGYEFFAK-RQLVTLFSAP
          DL.L.SDP.KDV.GWG.N.RGVSFTFGA.V..KFL..HD..LIC.AHQVVEDGYEFFA..RQ.VTLFS..
Retrocopy DL<LSSDPNKDVLGWGKNERGVSFTFGA*VIAKFLHKHDSNLICKAHQVVEDGYEFFAR<RQFVTLFSTS

Parental  NYCGEF
          NYCGEF
Retrocopy NYCGEF

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_707 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Sorex araneus	ENSSARG00000011890	2 retrocopies	retro_sara_236, retro_sara_707 ,