RetrogeneDB ID: retro_sara_348

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_174924:8280..8973(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK13
• Ensembl ID: ENSSARG00000006324
• Aliases: None
• Description: mitogen-activated protein kinase 13 [Source:HGNC Symbol;Acc:6875]

Sequence

>retro_sara_348
TACCTAGTGATGCCTTTTATGCAAACGGACCTGCAGAAGCTCATGGGCGTGGAGTTCAGTGAGGACAAAGTCCAGTTCCT
GGTATATCAGATGTTTAAGGGTCTCAAGTTATATCCACTCGGCGGGGGTTGTCCATAGGGACCTGAAGCCGGGCACCCTG
GCTGTGAACGAGGACTGTGAACTGAAGATCTTGGATTTGGGGCTGGCACGGCACGCGGATGCGGAAATGACGGGCTACGT
GGTGACAGGCTGGTACCGTGCCCCGGAGGTGATCCTCAGCTGGATGCACTACAACCAGACGGTGGATATCTGGTCTGTGG
GCTGCGTCATGGCTGGAGATGCTGACGGGCAGGACTCTGTTCAAAGGGAAAGATTACCTGGACCAGCTGTCGCGGATCCT
GAAGGTGACAGGGGTTGCCGGGCGCAGAGTTTGTCCAGAAGTTGAAGGATAAGGCGGCCAAACCCTACATCCAGTCCCTG
CCCCAGAGCCCCAAGAAGGACTTTTCTCAGCTCTTCCCACGTGCCAGCCCCGAGACCACCAACCTGCTGGATGTGGACAA
ACGTCTGACGGCCACGCAGGCCCTCGCCCATCCATTCTTCGAGCCCTTCCTGGAGCCCGAGGAGGAGCCGGTGGCCCTGC
AGCCCTTTGAAGATGCCTTGGAGCACGAGAAACTCACGGTGGACGAGTGGAAG

Alignment

ORF - retro_sara_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YLVMPFMQTDLQKLMGVEFSEDKVQYLVYQMFKGLK-YIHSAGVVHRDLKPGNLAVNEDCELKILDFGLA
          YLVMPFMQTDLQKLMGVEFSEDKVQ.LVYQMFKGLK.YIHSAGVVHRDLKPG.LAVNEDCELKILD.GLA
Retrocopy YLVMPFMQTDLQKLMGVEFSEDKVQFLVYQMFKGLK>YIHSAGVVHRDLKPGTLAVNEDCELKILDLGLA

Parental  RHADAEMTGYVVTRWYRAPEVILSWMNYNQTVDIWSVGCIMA-EMLTGRTLFKGKDYLDQLSQILKVTGV
          RHADAEMTGYVVT.WYRAPEVILSWM.YNQTVDIWSVGC.MA.EMLTGRTLFKGKDYLDQLS.ILKVTGV
Retrocopy RHADAEMTGYVVTGWYRAPEVILSWMHYNQTVDIWSVGCVMA>EMLTGRTLFKGKDYLDQLSRILKVTGV

Parental  -PGAEFVQKLKDKAAKSYIQSLPQSPKKDFSQLFPRASPEATDLLEKILELDVDKRLTATQALAHPFFEP
          .PGAEFVQKLKDKAAK.YIQSLPQSPKKDFSQLFPRASPE.T.LL.....L.....L........PF.EP
Retrocopy >PGAEFVQKLKDKAAKPYIQSLPQSPKKDFSQLFPRASPETTNLLDVDKRLTATQAL--AHPFFEPFLEP

Parental  FREPEEETVALQPFEDALENEKLTVDEWK
          ....EEE.VALQPFEDALE.EKLTVDEWK
Retrocopy ----EEEPVALQPFEDALEHEKLTVDEWK

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_348 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sorex araneus	ENSSARG00000006324	1 retrocopy	retro_sara_348 ,