RetrogeneDB ID: retro_itri_458

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393293.1:341826..342675(+)
• Located in intron of: ENSSTOG00000012807

Retrocopy information

• Ensembl ID: ENSSTOG00000028445
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK20
• Ensembl ID: ENSSTOG00000004663
• Aliases: None
• Description: cyclin-dependent kinase 20 [Source:HGNC Symbol;Acc:21420]

Sequence

>retro_itri_458
GTGGTGCAGCTAAAGCCCGTGTACCCGCATGGTGCAGGCTTCGTGCTGGCCTTTGAGTTCATGCTGTCAGACTTGGCAGA
GGTGGTGTGCCATGCCCAGAGGCCGCTGGCCCCAGCACAGGTCAAGAGCTACCTGCAAATGCTGCTCAAGGGTGTGGCCT
TCTGCCATGCCAACAACATTGTGCATCGGGATCTGAAAACTGCCAATCTGCTCATCAATGCTTCAGACCAGTTCAAGATA
GCAGACTTTGGTCTGGCCCAGGTCTTTTCTCCTGATGGCAGCCGCCTCTACACACACCAGGTGGCTACCAGGTGGTACCG
AGCCCCTGTGCTCCTGTATGGTGCCCGCCAATATGACCAGGGCGTTGACCTATGGGCTGTGGGCTGCATCATGGGGGAGC
TATTGAATGGGTCCCCTCTTTTCCCCGGAGAGAACGACATTGAACAGCTTTGCTGTGTGCTTCGCATCTTGGGCACCCCT
AGCCCTCAAGTCTGGCCAGAGATCACAGAGCTGCCAGACTACAACAAGATCTCCTTTAAGGAACAGGCGCCAATGCCCCT
GGAGGAGGTCCTGTCAGACGCCTCTCTTCAGGCCTTGGACCTGCTGAGTCAGTTCCTCCTCTACCCTCCTTGCCAGCGCG
TTGCAGCCTCCGAGGCTTTCCTGCATCAATACTTCTTCACAGCTCCCTTTCCCTCCCACCCATCTGAGCTGCCAATTCCC
CAGCGCCCAGGGGGGCCTGCTCCTAAGGCCCACCCGGGACCTCCTCATGTCCATGACTTCCATGTGGACCGGCCTCTTGA
GGAGTCACTGTGGGATCCAGAACTGATTTGGCCCTTTATCCCAGAGGGG

Alignment

ORF - retro_itri_458 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.23 %
• Parental protein coverage: 94.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVQLKAVFPHGAGFVLAFEFMLSDLAEVVRHAQRPLAPAQVKSYLQMLLKGVAFCHANNIVHRDLKPANL
          VVQLK.V.PHGAGFVLAFEFMLSDLAEVV.HAQRPLAPAQVKSYLQMLLKGVAFCHANNIVHRDLK.ANL
Retrocopy VVQLKPVYPHGAGFVLAFEFMLSDLAEVVCHAQRPLAPAQVKSYLQMLLKGVAFCHANNIVHRDLKTANL

Parental  LISASGQLKIADFGLARVFSPDGSRLYTHQVATRWYRAPELLYGARQYDQGVDLWAVGCIMGELLNGSPL
          LI.AS.Q.KIADFGLA.VFSPDGSRLYTHQVATRWYRAP.LLYGARQYDQGVDLWAVGCIMGELLNGSPL
Retrocopy LINASDQFKIADFGLAQVFSPDGSRLYTHQVATRWYRAPVLLYGARQYDQGVDLWAVGCIMGELLNGSPL

Parental  FPGENDIEQLCCVLRILGTPSPQVWPEITELPDYNKISFKEQAPVPLGEVLSDASLQALDLLGQFLLYPP
          FPGENDIEQLCCVLRILGTPSPQVWPEITELPDYNKISFKEQAP.PL.EVLSDASLQALDLL.QFLLYPP
Retrocopy FPGENDIEQLCCVLRILGTPSPQVWPEITELPDYNKISFKEQAPMPLEEVLSDASLQALDLLSQFLLYPP

Parental  RQRIAASQALLHQYFFTAPLPAHPSELPIPQRPGGPASKAHPGPPHVHDFHVDRPLEESLLDPELIRPFI
          .QR.AAS.A.LHQYFFTAP.P.HPSELPIPQRPGGPA.KAHPGPPHVHDFHVDRPLEESL.DPELI.PFI
Retrocopy CQRVAASEAFLHQYFFTAPFPSHPSELPIPQRPGGPAPKAHPGPPHVHDFHVDRPLEESLWDPELIWPFI

Parental  PKG
          P.G
Retrocopy PEG

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_458 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_458 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000004663	1 retrocopy	retro_itri_458 ,