RetrogeneDB ID: retro_itri_1674

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393624.1:790741..791358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VRK1
• Ensembl ID: ENSSTOG00000011492
• Aliases: None
• Description: vaccinia related kinase 1 [Source:HGNC Symbol;Acc:12718]

Sequence

>retro_itri_1674
GTTTCAAGAAAGGAATGGAAAGTAGGATTACCCATTGGCCAAGGTAGCTTTGACTGTTATATAGCTTGCTGATAAAAAAT
CTTTGAAATAAATTGACAACGAAACAACTCAGACTATAAAAGTAGAAACCAGTGACAATGAACCTTTTTTTTAAACTGAA
TTTAAAGTTCTCCCAGCAAGCTGCAAAACCAGAGCAAATTCAGAAATGGATTCATACCCATGAACTTTAGTACACTGGTG
TTTCTAAACATTAGGGGTTCTGGTCTACATAATAAAAATGCAAAAAGTTGCAGACTTATGTTAATTGATTGCTTTGGAAG
TGCCCTTCAGAAAATATATGAAGCAAATGCCAAAAGATTTTCTCAGAAAACTGTCTTGCAGCTAAGCTTACCAATTTTGG
ATACTCTGAAATATATTCATGAGCATGAATATGTACCTGGAGATATCAAGACCTCAAATCTTCTGATCTTTAGAAATCTT
GACCAAGTGTACTTGGTAGATTGTGGCCTTGCTTTCCAGTACTGTCCAGAAGAGATCATAAAGAATGTAAGGAGGACCCT
TAAAGATATCATGATAGCACTATTGAACTCAACAGCATTCATGCCCATCAAGACATA

Alignment

ORF - retro_itri_1674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 63.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSKKEWKLGLPIGQGGFGC-IYLADRNSSKSVGSDAPCVVKVEPSDN-GPLFTELK-FYQRAAKPEQIQK
          .S.KEWK.GLPIGQG.F.C.I.LAD..S.K..........KVE.SDN.....TE.K.F.Q.AAKPEQIQK
Retrocopy VSRKEWKVGLPIGQGSFDC>I*LADKKSLK*IDNETTQTIKVETSDNEXXXXTEFK>FSQQAAKPEQIQK

Parental  WVRTHKMKYLGVPKY-WGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLKLSLRILDILEY
          W..TH...Y.GV.K...GSGLH.KN.KS.R.M..D.FGS.LQKIYEANAKRFS.KTVL.LSL.ILD.L.Y
Retrocopy WIHTHEL*YTGVSKH>RGSGLHNKNAKSCRLMLIDCFGSALQKIYEANAKRFSQKTVLQLSLPILDTLKY

Parental  IHEHEYVHGDIKASNLLLSYKNPDQVYLVDYGLAYRYCPEGV-HKEYKEDPKRCHDGTLEFTSIDAHNGV
          IHEHEYV.GDIK.SNLL....N.DQVYLVD.GLA..YCPE...HKE.KEDP.R.HD.T.E..SI.AH...
Retrocopy IHEHEYVPGDIKTSNLLI-FRNLDQVYLVDCGLAFQYCPEEI<HKECKEDP*RYHDSTIELNSIHAHQDI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1674 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1674 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000018006	1 retrocopy	retro_drer_17,
Macropus eugenii	ENSMEUG00000012543	1 retrocopy	retro_meug_186,
Otolemur garnettii	ENSOGAG00000016785	1 retrocopy	retro_ogar_2000,
Ictidomys tridecemlineatus	ENSSTOG00000011492	1 retrocopy	retro_itri_1674 ,
Ictidomys tridecemlineatus	ENSSTOG00000022141	1 retrocopy	retro_itri_1378,