RetrogeneDB ID: retro_itri_1817

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393892.1:35882..36794(-)
• 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_1817
GCAATAATTATTCAGTCATTTATTCCAGGCTACAGAGAAAGAAAACAGCAATATTCCCTCCAGAGAAGTGCGTTCGATTT
CTGTGCACACTCAGCAGAGTCTGGTAGCACTTTCTCCATCACTAGTGCCCCCTACCGTACCCTCCTGGTAAGGCAGCTTC
TGTTTTTATACAAACAAAAGGAAGATGCAAAACAATTGATATGGCTGTATTAGAGCTTAATTAAACACAGCTCCCTGTTT
GTCAAGCAACTGGATGGATCTGAGAGACCTACATGCTTATTTCAGATAAAGAGGCTCATGAGTCTCTGTTGCAGGTGGCT
GCAGAGCTATAATGATGACAGTTTGAATGTTGCACTTCCAATGCGAAACCTTGAGGTCTTTTCCTCTGAGAATACTTCTT
TGCCAGTTTTACTAGATGCTAGCTATGTGGTGTCAGTAATTGAACAGGTTTTGCACTACGTGATCCACAATGGGTATTAT
AGGTCTCTCTATTTGTTGATTAATAGCAAGCTTCCATCAAGTATTGAATATTCTGATTTATCACGAGTTCCTATAGCAAA
CATTTTGCTGGAGAATGTCCTAAAACCATTGCACTTTACCTACAGCTCCTGCACAGAAGGTGCAAGGCAGCAAGTTTTTT
CAGCCTTCACAGAGGAGTTTCTGGCAGCACCTTTCACAGATCAGATTTTCTGCTTGTCATTCTGGCATTAGCAGATGTAC
AGACCGTTTCCCCTTATGAGCCCTTTCTGAATGCACTATTGTTACTAGAGAGTAGATGTTCAAAAAGGAGTGGTGGAGCA
CCTGGCTTTTCTATTTTGTTTTAACTGTTGGTGAAAATGACTTGGGGGTGCTCTCTGAGGAGGGCCTGCTGGTGTATCTG
CACGTGCTCCAGATTTTCTCAGTTACCTGCCT

Alignment

ORF - retro_itri_1817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.64 %
• Parental protein coverage: 72.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AIIIQSFIRGYRDRKQQYSLQRSAFDRCAHSAQSGGTFSITNAPNLTLLVRQLLFFYKQSEDAKRLIWLY
          AIIIQSFI.GYR.RKQQYSLQRSAFD.CAHSA.SG.TFSIT.AP..TLLVRQLLF.YKQ.EDAK.LIWLY
Retrocopy AIIIQSFIPGYRERKQQYSLQRSAFDFCAHSAESGSTFSITSAPYRTLLVRQLLFLYKQKEDAKQLIWLY

Parental  QNLIKHSSLFVKQLDGSERPTCLFQIKRLMSLCCRLLQSCNDDSLNVALPMRMLEVFSSENTYLPVLQDA
          ..LIKHSSLFVKQLDGSERPTCLFQIKRLMSLCCR.LQS.NDDSLNVALPMR.LEVFSSENT.LPVL.DA
Retrocopy *SLIKHSSLFVKQLDGSERPTCLFQIKRLMSLCCRWLQSYNDDSLNVALPMRNLEVFSSENTSLPVLLDA

Parental  SYVVSVIEQILHYMIHNGYYRSLYLLINSKLPSSIEYSDLSRVPIAKILLENVLKPLHFTYSSCPEGARW
          SYVVSVIEQ.LHY.IHNGYYRSLYLLINSKLPSSIEYSDLSRVPIA.ILLENVLKPLHFTYSSC.EGAR.
Retrocopy SYVVSVIEQVLHYVIHNGYYRSLYLLINSKLPSSIEYSDLSRVPIANILLENVLKPLHFTYSSCTEGARQ

Parental  QVFSAFTEEFLAAPFTDQI-FRFVIPALADVQTAFPYEPFLNALLLLESRCSKRSRGAP-WLFYFVLTVG
          QVFSAFTEEFLAAPFTDQI.F..VI.ALADVQT..PYEPFLNALLLLESRCSKRS.GAP.WLFYFVLTVG
Retrocopy QVFSAFTEEFLAAPFTDQI<FLLVILALADVQTVSPYEPFLNALLLLESRCSKRSGGAP<WLFYFVLTVG

Parental  ENYLGVLSEEGLLVYLHVLQ-TFLSQLP
          EN.LGVLSEEGLLVYLHVLQ..FLS.LP
Retrocopy ENDLGVLSEEGLLVYLHVLQ<DFLSYLP

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_1817 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1817 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,