RetrogeneDB ID: retro_sara_80

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_2249:42473..43241(-)
• Located in intron of: ENSSARG00000012385

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASH2L
• Ensembl ID: ENSSARG00000002606
• Aliases: None
• Description: ash2 (absent, small, or homeotic)-like (Drosophila) [Source:HGNC Symbol;Acc:744]

Sequence

>retro_sara_80
CCTGGGAGCAAGGACCCGGAGGAAGATTATCCGAAATTTGGACTCTTGGACCAGGATCTTAGTAACATCGGTCCTGCTTA
TGATAACCAAAAGCAAAGCAGTGCCATGTCTACTGGTGGAAATCTAAACGGGGGAGTTACTGCAGGAAGCAGTGGGAAAG
GAAGAGGAGCGAAGCGCAAACAGCAGGACGGAGGAGCCACGGGGACCACCAAGAAGGCTCGGAGTGATCCTTTGTGTTCT
GCCCAGCGCCTGCCCCCTCATGGCTACCCCTTGGAGCACCCATTTAACAAGGATGGCTACCGGTATATTCTGGCGGAGCC
CGACCCCCATGCCCCTGACCCGGAGAAGCTGGAGCTCGCCTGTTGGGCAGGGAAACCTATCCCTGGCGACCTGCACAGAG
CCTGCCTGTATGAACGGCTCTTGTTAGCCCTGCATGATCGAGCTCCCCGGTTAAAGATCTCTGATGACCGGCTGACTGTG
GTTGGAGAGAAGGGCTCCTCCACGCTTCGGGCTGCTCACGGGGTGCGGAAGGGCGCCTGGTACTTCGAGATCACCGTGGA
CGAGATGCCGCCCGACACTGCTGCCCGGCTGGGGTGGTCCCAGCCCTTAGGTAACCTTCAGGCTCCCTTAGGTTATGATA
AATTTAGCTATTCTTGGCGGAGCAAAAAAGGGACCAAGTTTCACCAATCTATTGGCAAACACTACTCGTCCGGCTATGGG
CAGGGAGACGTCCTGGGGTTCTACATCAATCTTCCTGAAGACACAGAC

Alignment

ORF - retro_sara_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.31 %
• Parental protein coverage: 52.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGSKDPEEDYPKLGLLDQDLSNIGPAYDNQKQSSAMSTGGNLNGGVTAGSSGKGRGAKRKQQDGGTTGTT
          PGSKDPEEDYPK.GLLDQDLSNIGPAYDNQKQSSAMSTGGNLNGGVTAGSSGKGRGAKRKQQDGG.TGTT
Retrocopy PGSKDPEEDYPKFGLLDQDLSNIGPAYDNQKQSSAMSTGGNLNGGVTAGSSGKGRGAKRKQQDGGATGTT

Parental  KKARSDPLFSAQRLPPHGYPLEHPFNKDGYRYILAEPDPHAPDPEKLELDCWAGKPIPGDLYRACLYERV
          KKARSDPL.SAQRLPPHGYPLEHPFNKDGYRYILAEPDPHAPDPEKLEL.CWAGKPIPGDL.RACLYER.
Retrocopy KKARSDPLCSAQRLPPHGYPLEHPFNKDGYRYILAEPDPHAPDPEKLELACWAGKPIPGDLHRACLYERL

Parental  LLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPL
          LLALHDRAP.LKISDDRLTVVGEKG.S..RA.HGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPL
Retrocopy LLALHDRAPRLKISDDRLTVVGEKGSSTLRAAHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPL

Parental  GYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTE
          GYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDT.
Retrocopy GYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTD

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_80 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
Oryctolagus cuniculus	ENSOCUG00000029521	2 retrocopies	retro_ocun_872, retro_ocun_897,
Sorex araneus	ENSSARG00000002606	1 retrocopy	retro_sara_80 ,