RetrogeneDB ID: retro_sara_337

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_170313:10709..11237(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VRK1
• Ensembl ID: ENSSARG00000009110
• Aliases: None
• Description: vaccinia related kinase 1 [Source:HGNC Symbol;Acc:12718]

Sequence

>retro_sara_337
ATCAAGGCCTCAAATTTTCTTTGAGCATCAAATCCCTGGCCAGGTGTATTTGATCAATTATGGCCTGGCTCATTGCTACT
GCCCAGAATGGATTCACAATGAGTACAACAAAGACCTGAAGAAATGTCACAATGGCACTTTGGAGTTCACCAGCATGGAT
GCACACGTGGCATGGCCCCATCAAGATGTGGTGATTTGGAAATACTTGCTTATTGCATAATCCAGTGGCTTAGCTGCCAC
CTTTCTTGGAAGGATAATTTAAAAGACCCCAAATATGTTAGAGATTCCAAAACTACATAGAAAATATTGCAAGTTTGATG
GACTATGTTTTCCTGAGAAAAACAAATCAGGTGACATTACTAAATACTTGAAACAGTGACATTACTGGACTGTGTTTAGA
AACCTCTTTATCAAAATCTATGAGATATTCTTTTGCAAGGACTAAAAGCTACAAGAAGTAAGGATGATGGCAAACCGGAC
CTCAGTATTGTGGGGAGTGGAGGTTTGAAAGCAAAAACCATAACAAAG

Alignment

ORF - retro_sara_337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.2 %
• Parental protein coverage: 52.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  IKASNLL-LSVKN-PDQVYLVDYGLAYRYCPEGVHKEYREDPKRCHDGTLEFTSIDAH-NGVAPSRRGDL
          IKASN.L.LS.K..P.QVYL..YGLA..YCPE..H.EY..D.K.CH.GTLEFTS.DAH..G.APSR.GDL
Retrocopy IKASNFL<LSIKS<PGQVYLINYGLAHCYCPEWIHNEYNKDLKKCHNGTLEFTSMDAH<RGMAPSRCGDL

Parental  EILGYCMIQWLSGHLPWEDNLKDPNYVRDSKIR-YREIASLMDK-CFPEKNKPGEIAKYL-ETVKFLDYA
          EIL.YC.IQWLS.HL.W.DNLKDP.YVRDSK......IASLMD..CFPEKNK.G.I.KYL.ETV..LD..
Retrocopy EILAYCIIQWLSCHLSWKDNLKDPKYVRDSKTT<IENIASLMDY<CFPEKNKSGDITKYL<ETVTLLDCV

Parental  EKPLYQNLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITK
          .KPLYQNL.DILLQGLKA..SKDDGK.DLS.V..GGLKAKTITK
Retrocopy *KPLYQNL*DILLQGLKATRSKDDGKPDLSIVGSGGLKAKTITK

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_337 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
Cavia porcellus	ENSCPOG00000001772	1 retrocopy	retro_cpor_1214,
Danio rerio	ENSDARG00000018006	1 retrocopy	retro_drer_17,
Macropus eugenii	ENSMEUG00000012543	1 retrocopy	retro_meug_186,
Sorex araneus	ENSSARG00000005475	1 retrocopy	retro_sara_33,
Sorex araneus	ENSSARG00000009110	2 retrocopies	retro_sara_287, retro_sara_337 ,
Sorex araneus	ENSSARG00000011446	1 retrocopy	retro_sara_518,