RetrogeneDB ID: retro_sara_236

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_120731:245..918(-)
• 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_236
GATAACTTCGACTTTTTTGAGCATGGTGGTTTCCCTCCAGAAAGCAACTACCTGGTTCCTGGGGAATATGTGGACAGGGG
GAAGCAGTTGCTGAGGACTATCTGCCTCTTACTGGCTTACAAAATCAAATGTCACGAGAATTTTTTTTCTTCTCACAGGA
AACCATGAATGTGCCAGCATCAATGGGATTTATGGATTTTATGACGAATGTAAAAGAAGATACAACATTAAACTATGGAA
AACTTTCACAGATTGCTTTAACTGTTTACCGATAGCCGCCATCATGGACGAGAAGCTACTCTGCTGTCATGGAGTTTTAT
CACCAGATCTTCAAATCTATGGAGCAGATACGGTGAATTATGTGACCAACTGATGTACCAGATCAAGGTCTTCTTTGTGA
TCTTTTGTGGTCTGACCCTAATAAAGATGTCTTAGGCTGGGGTGAAAATGACAGAGGAGTGTCCTTCACATTTGGTGCAG
AAGTGGTTGCAAAATTTCTCCATAAGCATGATTTGGCTCTTATGTGTAGAGCCCATTAAGTGGTTGAAGATGGATATGAG
TTTTTTGCCAAGAGGCAGTTGACCACTCTGTTTTCCGCACCCAATTATTGTGGAGAGTTTGACAATGCCGGCTCATGATG
AGTGTGGACGAGACGGTAATGTGCTCATTTCAG

Alignment

ORF - retro_sara_236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 96.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLLRLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFF-LLRGNHECASINRIYGFYDE
          D....FE.GGFPPE.NYL..G.YVDRGKQ.L.TICLLLAYKIK..E....LL.GNHECASIN.IYGFYDE
Retrocopy DNFDFFEHGGFPPESNYLVPGEYVDRGKQLLRTICLLLAYKIKCHEXXX>LLTGNHECASINGIYGFYDE

Parental  CKRRFNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQ-SMEQIRRIMRPTDVPDTGLLCDLLWSD
          CKRR.NIKLWKTFTDCFNCLPIAAI.DEK..CCHG.LSPDLQ.SMEQIR.IM.PTDVPD.GLLCDLLWSD
Retrocopy CKRRYNIKLWKTFTDCFNCLPIAAIMDEKLLCCHGVLSPDLQ>SMEQIR*IM*PTDVPDQGLLCDLLWSD

Parental  PDKDVQGWGENDRGVSFTFGADVVSKFLNRHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDN
          P.KDV.GWGENDRGVSFTFGA.VV.KFL..HDL.L.CRAH.VVEDGYEFFAKRQL.TLFSAPNYCGEFDN
Retrocopy PNKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLALMCRAH*VVEDGYEFFAKRQLTTLFSAPNYCGEFDN

Parental  AGG-MMSVDETLMCSFQ
          AG..MMSVDET.MCSFQ
Retrocopy AGS<MMSVDETVMCSFQ

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_236 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,