RetrogeneDB ID: retro_itri_1848

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394084.1:85845..86482(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE3C
• Ensembl ID: ENSSTOG00000001669
• Aliases: None
• Description: ubiquitin protein ligase E3C [Source:HGNC Symbol;Acc:16803]

Sequence

>retro_itri_1848
AACAGCTCCCTGTTTGTCAAGCAACTGAATGGATCCGAGAGACCGAAATGCTTATTTCAGATAAAGAGGCTCATGAGCCT
CTGTTGCAGGTGGCTGCAGAGCTGTAATGATGACAGTTTGAATGTCGCACTTCCACTGAGAATGCTTGAGGTCTTTTCCT
CTGAGAATACTTCCTTGCCTGTTTACTAGATGCTAGCTATGAGGTGTCAGTAATTGAACAGGTTTTGCACTACATGAAAC
ACAATGGGTATTATAGTCTCTCTATTTGTTGATTAACAGCAAGATTCCATCAAGTATTGAATATTCCGATTTATCTATAG
CAAACATTTTGCTGGGGAGTGTCCTAAACCGTTGCACTTTACCTACAGCTCCTGCCCAGAAGGTGCAAGGCAGCAAGTTT
TTTGAGCCTTCACAGAGGAGTTTTTGGCAGCACCTTTTACAGATCAGATTTTCCGCTTGTCATTCTGGCATTAGCAGATG
TACAGACCGTTTTCCCTTAAGAGCCCTTTCTGAATGCACTATTGTTACTAGAGAGTAGATGTTCAAAAAGGAGTGGTGGA
GCACCTGGCTTTTCTATTTTGTTTTAACTGTTGGCAAAAATGACTTGGGGGTGCTCTCTGAGGAGGGCCTGCTGGTA

Alignment

ORF - retro_itri_1848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.59 %
• Parental protein coverage: 51.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HSSLFVKQLDGSERPTCLFQIKRLMSLCCRLLQSCNDDSLNVALPMRMLEVFSSENTYLPV-LQDASYVV
          .SSLFVKQL.GSERP.CLFQIKRLMSLCCR.LQSCNDDSLNVALP.RMLEVFSSENT.LPV.L.DASY.V
Retrocopy NSSLFVKQLNGSERPKCLFQIKRLMSLCCRWLQSCNDDSLNVALPLRMLEVFSSENTSLPV<LLDASYEV

Parental  SVIEQILHYMIHNGYYR-SLYLLINSKLPSSIEYSDLSRVPIAKILLENVL-KPLHFTYSSCPEGARWQV
          SVIEQ.LHYM.HNGYY..SLYLLINSK.PSSIEYSDLS...IA.ILL..VL.KPLHFTYSSCPEGAR.QV
Retrocopy SVIEQVLHYMKHNGYYS<SLYLLINSKIPSSIEYSDLS---IANILLGSVL<KPLHFTYSSCPEGARQQV

Parental  FSAFTEEFLAAPFTDQIFR-FVIPALADVQTAFPYEPFLNALLLLESRCSKRSRGAP-WLFYFVLTVGEN
          F.AFTEEFLAAPFTDQIFR..VI.ALADVQT.FP.EPFLNALLLLESRCSKRS.GAP.WLFYFVLTVG.N
Retrocopy F*AFTEEFLAAPFTDQIFR<LVILALADVQTVFP*EPFLNALLLLESRCSKRSGGAP<WLFYFVLTVGKN

Parental  YLGVLSEEGLLV
          .LGVLSEEGLLV
Retrocopy DLGVLSEEGLLV

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_1848 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1848 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000000964	1 retrocopy	retro_ogar_3065,
Ictidomys tridecemlineatus	ENSSTOG00000001669	3 retrocopies	retro_itri_1547, retro_itri_1817, retro_itri_1848 ,