RetrogeneDB ID: retro_itri_245

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:23015762..23016218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000028886
• Aliases: None
• Description: None

Sequence

>retro_itri_245
GGCCTCGGAGGAGCAGTGGTGGTCACGCTCTATAAGATGGGGTTTCCGGAAGCTGCCAGGACACATCAGATTGAGGCTGC
TCCTACCAGTGCTGCAAGTGATGGATTTAAGGCAGATCTTGTCTTTAAGGAGATCGAGAAGAAGCTTGAAGAGGATGGGG
AACAGTTTGTGAAGAAAATTGGTGGTATTTTTGCCTTCAAGGTGAAGGATGGTCCTGGGGGTAAAGAAGCCACCTGGGTG
GTGGATGTGAAGAATGGCAAAGGATCAGTGCTTCCCAACTCAGATAAGAAGGCTGACTGCACAATCACCATGGCTGACTC
GGACTTACTGGCTTTAATGACTGGTAAAATGAATCCTCAGTCGGCCTTCTTTCAAGGCAAATTGAAAATCACTGGCAACA
TGGGGCTGGCAATGAAGTTACAAAATCTTCAACTTCAACCAGGCAAAGCTAAGCTG

Alignment

ORF - retro_itri_245 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.79 %
• Parental protein coverage: 82.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLGGAVVVTLYKMGFPEAASNFITTHQIEAAPTSAASDGFKADLVFKEIEKKLEEDGEQFVKKIGGIFAF
          GLGGAVVVTLYKMGFPEAA.....THQIEAAPTSAASDGFKADLVFKEIEKKLEEDGEQFVKKIGGIFAF
Retrocopy GLGGAVVVTLYKMGFPEAAR----THQIEAAPTSAASDGFKADLVFKEIEKKLEEDGEQFVKKIGGIFAF

Parental  KVKDGPGGKEATWVVDVKNGKGSVLPNSDKKADCTITMADSDLLALMTGKMNPQSAFFQGKLKITGNMGL
          KVKDGPGGKEATWVVDVKNGKGSVLPNSDKKADCTITMADSDLLALMTGKMNPQSAFFQGKLKITGNMGL
Retrocopy KVKDGPGGKEATWVVDVKNGKGSVLPNSDKKADCTITMADSDLLALMTGKMNPQSAFFQGKLKITGNMGL

Parental  AMKLQNLQLQPGKAKL
          AMKLQNLQLQPGKAKL
Retrocopy AMKLQNLQLQPGKAKL

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_245 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_245 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000013683	1 retrocopy	retro_itri_1320,
Ictidomys tridecemlineatus	ENSSTOG00000028886	1 retrocopy	retro_itri_245 ,