RetrogeneDB ID: retro_itri_1884

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394599.1:8485..8890(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX3
• Ensembl ID: ENSSTOG00000002108
• Aliases: None
• Description: Y box binding protein 3 [Source:HGNC Symbol;Acc:2428]

Sequence

>retro_itri_1884
GTACATCAGACTGCCATCAAGAAGAATAACCCACGGAAATATCTGCGTAGTGTAGGAGATGGAGAAACTGTAGAGTTTGA
TGTGGTTGAAGGAGAAAAGGGTGCTGAAGCAGCCAATGTGACTGGCCCAGATGGAGTTCCTGTGGAAGGGAGTCGATATG
CTGCTGATCGCCGCCGTTATAGACGTGGCTACTAAGGCAGACGCCGTGGACCTCCCCGTAATTACGCTGGGGAGGAGGAG
GAGAAAGGGAGCGGCAGCAGTGAAGGATTTGACCCCCCTGCCACTGACGGGCAGTTCTCTGGGGCCCGGAGTCAGCTGCG
CCGCCCCCAGTATCGCCCTCAGTACTGGCAGCGGCGGTTCCCGCCTTACCACGTGGGACAGACCTTTGACCGTCCCAACA
GAATG

Alignment

ORF - retro_itri_1884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.56 %
• Parental protein coverage: 51.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAADRRRYRRGYYGRRRG
          VHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAADRRRYRRGY.GRRRG
Retrocopy VHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAADRRRYRRGY*GRRRG

Parental  PPRNYAGEEEEEGSGSSEGFDPPATDGQFSGARSQLRRPQYRPQYRQRRFPPYHVGQTFDRRSRV
          PPRNYAGEEEE.GSGSSEGFDPPATDGQFSGARSQLRRPQYRPQY.QRRFPPYHVGQTFDR..R.
Retrocopy PPRNYAGEEEEKGSGSSEGFDPPATDGQFSGARSQLRRPQYRPQYWQRRFPPYHVGQTFDRPNRM

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_1884 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1884 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002557	1 retrocopy	retro_etel_1898,
Microcebus murinus	ENSMICG00000004602	1 retrocopy	retro_mmur_337,
Ictidomys tridecemlineatus	ENSSTOG00000000116	1 retrocopy	retro_itri_1532,
Ictidomys tridecemlineatus	ENSSTOG00000002108	1 retrocopy	retro_itri_1884 ,