RetrogeneDB ID: retro_sara_287

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_148084:10158..10707(+)
• 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_287
GATATGAATTCTTCAAAATTCGTTGGCAGTGATGCACCCTGTATTGTAAAAGTGGAACCTAGTGACAGTGGACCTCTTTT
TACTGAATTAAAATTCTACCAGCAAGATGCCAAACCAGATCAAATTCAGAAATGGCTTCACACTCATACACTTAAATACC
TGGGCATGCCTAAGTATTTGGGGGGGTCTGACCTTTATGAGAGAATGGAAGAAGTGACAGGTTTATGATAATGGACAGCT
TTGCGGGTAACCTTTAGAAAATATATGAAGTAAATGCCAAAAGGTTTTTTTTTTTTTTGAAAACTGTCTTGCAGCTAACC
TTGGAATTCTGGATACCCTGGTATATATCCATGAGCATGAGTACATACATGAGTACATCTCAAGGCCATCAATCTTCTTT
TGAATATCAAAAACCCTGACCAGGTGTACTGGGTCCATTATGGCCTTGCTTATCGCTAGTGCTCAGAAGGGATTCATAAA
GAGTATCAAAAAGACCTAAAGAGATGTCACAATGGCACTTTGGAGTTCACCAGCATTGACACTCAGAGT

Alignment

ORF - retro_sara_287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.31 %
• Parental protein coverage: 52.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DTNSSKSVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKAEQIQKWIRARKLRYLGVPKYWG--SLHEK-N
          D.NSSK.VGSDAPC.VKVEPSD.GPLFTELKFYQ..AK..QIQKW.....L.YLG.PKY.G...L.E..N
Retrocopy DMNSSKFVGSDAPCIVKVEPSDSGPLFTELKFYQQDAKPDQIQKWLHTHTLKYLGMPKYLGGSDLYER<N

Parental  GRSYRFMIMDRFGSDLQKIYEANAKR--FSRKTVLQLSLR-ILDILEYIHEHEYVHGDIKASNL-LL-SV
          GRS.RFMIMD.F...L.KIYE.NAKR.....KTVLQL.L..ILD.L.YIHEHEY.H..I......LL...
Retrocopy GRSDRFMIMDSFAGNL*KIYEVNAKRXXXXXKTVLQLTLE<ILDTLVYIHEHEYIHEYISRPSI<LLLNI

Parental  KNPDQVYLVDYGLAYRYCPEGVHKEYREDPKRCHDGTLEFTSIDAHN
          KNPDQVY.V.YGLAYR.C.EG.HKEY..D.KRCH.GTLEFTSID...
Retrocopy KNPDQVYWVHYGLAYR*CSEGIHKEYQKDLKRCHNGTLEFTSIDTQS

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_287 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,