RetrogeneDB ID: retro_sara_452

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_213384:149..574(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX12
• Ensembl ID: ENSSARG00000001830
• Aliases: None
• Description: sorting nexin 12 [Source:HGNC Symbol;Acc:14976]

Sequence

>retro_sara_452
AATTCAAAGCCACAGAATCTGACGGATGCTTATGCATTGCCAAGTGACTTCCCGAAGATCAATGTCTTTAATCCACAGAT
GGTGGGCACAAGCCAGGCACACTCCATCACTTCTGAGGTTTGCATGTGGACAAAGCACCTATCTTCAAGCTGAAGGCACC
CTGTGTACAGTGGCACTACAGTGATTTTACATGGCTCAAAAATTTCCTAGAGTATGATGGTAAGGTTGTAGTACCACCAC
TTACCGGGAAAGGCTTGAAGCTGGCAGTATCCTTTTTGAGGAAACAAAGGTACCTTTGAGAAGTCCTTCATTGAAGAAAG
AAGGCAGGGCCCAGGACAATCTATTAACAAAATTGCTACACATTCACTGGTTCCGAGACAACCTGCCTGCATGCGTTCCT
GCAGGAGGAGAAAACTGACAGGAAC

Alignment

ORF - retro_sara_452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.38 %
• Parental protein coverage: 89.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NSKPQDLTDAYGPPSNFLDIDIFNPQTVGVGRARFTTYEVRMRTN-LPIFKLKESCVRRRYSDFEWLKNE
          NSKPQ.LTDAY..PS.F..I..FNPQ.VG...A...T.EV.M.T...PIFKLK..CV...YSDF.WLKN.
Retrocopy NSKPQNLTDAYALPSDFPKINVFNPQMVGTSQAHSITSEVCMWTK<APIFKLKAPCVQWHYSDFTWLKNF

Parental  LERDSKMVVPPLPGKALKR-QLPFRGAEGIFEESFIKERRQGLAQFINKIAGHPLAQNE-CCLHMFLQEE
          LE.D.K.VVPPL.GK.LK..Q.PF.G..G.FE.SFI.ERRQG..Q.INKIA.H.L......CLH.FLQEE
Retrocopy LEYDGKVVVPPLTGKGLKL>QYPF*GNKGTFEKSFIEERRQGPGQSINKIATHSLVPRQ<TCLHAFLQEE

Parental  AMDRN
          ..DRN
Retrocopy KTDRN

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_452 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007871	1 retrocopy	retro_btau_1080,
Dasypus novemcinctus	ENSDNOG00000018281	1 retrocopy	retro_dnov_9,
Oryctolagus cuniculus	ENSOCUG00000014919	1 retrocopy	retro_ocun_1286,
Otolemur garnettii	ENSOGAG00000008973	1 retrocopy	retro_ogar_2565,
Rattus norvegicus	ENSRNOG00000004036	2 retrocopies	retro_rnor_1751, retro_rnor_501,
Sorex araneus	ENSSARG00000001830	1 retrocopy	retro_sara_452 ,