RetrogeneDB ID: retro_itri_1547

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393537.1:55665..56655(+)
• 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_1547
GCAATAATTATTCAGCCATTTATTCCAGGTTACAGAGACAGAAAACAGCAATATTCTCTCCAGAGAAGTGCGTTCGATTT
CTGTGCACACTTGGCAGAGTCTGGTAGCACTTACTCCATTACTAATGCCCCCTATCTTACCCTCCTGGTAAGGCAGCTTC
TGTTTTCATACAAACAAAACCAAGATGCAAAACGATTGATATGGCTGCATTAGAGCTTAATTAAACACAGCTCCCTGTTT
GTCAAGCAAGTGGGTGGATCCGAGTGACCAACATGCTTATTTCAGATAAAGAGGCTCATGAGCCTCTATTGCAGGTGGCT
GCAGAGCTGTAATCATGACAGTTTGAATGTTGCACTTCCAATGCGAATGCTTGAGGTCTTTTCCTCTGAGAATACTTCCT
TGCCTGTTTTACTAGATGCTAGCTATGTGGTGTCAGTAATTGAACAGGTTTTGCACTACATGATCCACAATGGGTATTAT
AGTCTCTCTATTTGTTGATTACCAGCAAGCTTCCATCAAGTATTGAATATTCTGATTTATTCCGAGTTCCTATAGGAAAC
ATTTTACTGGAGAATGTCCTAAAACCGTTGCAGTTTACCTACAGCTCCTGCCCAGAAGGTGCAAGGCAGCAAGTTTTTTC
AGCCTTCACAGAGGAGTTTCTGGCAGTACCTTTCACAGATCAGATTTTCTGCTTGTCATTCTGGCATTAGCAAATGTACA
GACTGTTTTCCCTTAAGAGCCCTTTCTGAATGCACTATTGTTACTAGAGAGTAGATGTTCAAAAAGGAGTGGTGGAGCAT
CTGGCTTTTCTATTTTGTTTTAACTGTTGGCGAAAATGACTTGGGGGTGCTCTCTGAGGAGGGCCTGCTGGTGTATCTGC
ACGTGCTCCAGACTTTCCTCTCCCAGTTACCTGCCTCCCCTGCAGGTGCCAGCTCCCAGGACTCCACCAGGGACTCTGAG
AACGAGAGTGAGGAGGCTGACAAGCCCGCC

Alignment

ORF - retro_itri_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 78.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AIIIQSFIRGYRDRKQQYSLQRSAFDRCAHSAQSGGTFSITNAPNLTLLVRQLLFFYKQSEDAKRLIWLY
          AIIIQ.FI.GYRDRKQQYSLQRSAFD.CAH.A.SG.T.SITNAP.LTLLVRQLLF.YKQ..DAKRLIWL.
Retrocopy AIIIQPFIPGYRDRKQQYSLQRSAFDFCAHLAESGSTYSITNAPYLTLLVRQLLFSYKQNQDAKRLIWLH

Parental  QNLIKHSSLFVKQLDGSERPTCLFQIKRLMSLCCRLLQSCNDDSLNVALPMRMLEVFSSENTYLPVLQDA
          ..LIKHSSLFVKQ..GSE.PTCLFQIKRLMSL.CR.LQSCN.DSLNVALPMRMLEVFSSENT.LPVL.DA
Retrocopy *SLIKHSSLFVKQVGGSE*PTCLFQIKRLMSLYCRWLQSCNHDSLNVALPMRMLEVFSSENTSLPVLLDA

Parental  SYVVSVIEQILHYMIHNGYYR-SLYLLINSKLPSSIEYSDLSRVPIAKILLENVLKPLHFTYSSCPEGAR
          SYVVSVIEQ.LHYMIHNGYY..SLYLLI.SKLPSSIEYSDL.RVPI..ILLENVLKPL.FTYSSCPEGAR
Retrocopy SYVVSVIEQVLHYMIHNGYYS<SLYLLITSKLPSSIEYSDLFRVPIGNILLENVLKPLQFTYSSCPEGAR

Parental  WQVFSAFTEEFLAAPFTDQI-FRFVIPALADVQTAFPYEPFLNALLLLESRCSKRSRGAP-WLFYFVLTV
          .QVFSAFTEEFLA.PFTDQI.F..VI.ALA.VQT.FP.EPFLNALLLLESRCSKRS.GA..WLFYFVLTV
Retrocopy QQVFSAFTEEFLAVPFTDQI<FLLVILALANVQTVFP*EPFLNALLLLESRCSKRSGGAS<WLFYFVLTV

Parental  GENYLGVLSEEGLLVYLHVLQTFLSQLPASPAGASSHDSTSDSEDESEEADKPA
          GEN.LGVLSEEGLLVYLHVLQTFLSQLPASPAGASS.DST.DSE.ESEEADKPA
Retrocopy GENDLGVLSEEGLLVYLHVLQTFLSQLPASPAGASSQDSTRDSENESEEADKPA

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_1547 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1547 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,