RetrogeneDB ID: retro_sara_59

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_1749:9387..9821(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSSARG00000011194
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_sara_59
GAATTTACAAGCTCAGGTTCCGCCAACACAGAGACCACCAAGGTGACAGGCAGCCTGGAAACCAAGTACCGGTGGGCCAA
GTATGGGCTCGGGTTCACTGAGAATTGGACCACGGACAACACGCTAGGCACCGAGATCACCGTAGAAGGCCAGCTCGCAC
GTGGCCTGAAGCGGACCTTTGAGTCATTCTTCTCTCCAAACACTGGGAAGAAAAATGCTAAAATCAAGACAGGGTACAAG
CGGGAGCACATCAACCTGGGCTGCGACGTGGATTTCAACATCGCTGGGCCTTCCATCCGGGCGCCCCCGTGCTGGCCCAG
GAGGGCTGGCTGGGGGGCTACCAGATGAACTTTGAGACTGCCAAGTCACGCGTGACCCAGCGCAACTTTGCGGTCGGCCA
CAAGACTGATGAGTTCCAGCTTCACACGAAGGTA

Alignment

ORF - retro_sara_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.07 %
• Parental protein coverage: 51.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFSTSGSSNTDTGKVTGTLETKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGK
          EF..SGS.NT.T.KVTG.LETKY.W..YGL.FTE.W.TDNTLGTEI..E.Q...GLK.TF...FSPNTGK
Retrocopy EFTSSGSANTETTKVTGSLETKYRWAKYGLGFTENWTTDNTLGTEITVEGQLARGLKRTFESFFSPNTGK

Parental  KSGKIKSSYKRECINLGCDIDFDFAGPAIH-GSAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDF
          K..KIK..YKRE.INLGCD.DF..AGP.I..G..V...EGWL.GYQM.F..AKS..T..NFAVG..T..F
Retrocopy KNAKIKTGYKREHINLGCDVDFNIAGPSIR<GAPVLAQEGWLGGYQMNFETAKSRVTQRNFAVGHKTDEF

Parental  QLHTNV
          QLHT.V
Retrocopy QLHTKV

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_59 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 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sorex araneus	ENSSARG00000008221	6 retrocopies	retro_sara_115, retro_sara_327, retro_sara_355, retro_sara_533, retro_sara_668, retro_sara_702,
Sorex araneus	ENSSARG00000011194	2 retrocopies	retro_sara_300, retro_sara_59 ,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,