RetrogeneDB ID: retro_itri_953

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393348.1:8278368..8278719(-)
• Located in intron of: ENSSTOG00000028127

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTGES
• Ensembl ID: ENSSTOG00000004909
• Aliases: None
• Description: prostaglandin E synthase [Source:HGNC Symbol;Acc:9599]

Sequence

>retro_itri_953
CTCCCCCCAAGCCTGGCAATGGTGAGTGGGCAGGTGTTCTCAGCCTTCATGCTTTGTAGTACATTACTGGTCATCAAGAT
GTATGTGGTGGCAGTCATCACAGGCCAAGTGAGGCTGCCGAAGAAGGCTTTTGCCAACCCTAAGGATGATTTGAGACAAG
GAGACCTTCAGTATTGCTGGAGCTACTCTGATGTGCAATTTTGCCTCAGAACCCACTGGAATGACGTGGAGACTATCTAC
CTTTTCTTCTTCCTGGGCCTTGTCTATACTTTCCTGGGGCCTGACCCTTTTCTTCATCTGAATGTACTTCTCATATTCCT
CCTGGGCCTTGTATTGCACACTGTGGCCTAC

Alignment

ORF - retro_itri_953 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 76.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTPSLATVSGPTLPAFLLCSTLLVIKMYVVAVITGQVRLRKKAFANPEDALRHGGLQFCRSDPDVERCLR
          L.PSLA.VSG....AF.LCSTLLVIKMYVVAVITGQVRL.KKAFANP.D.LR.G.LQ.C.S..DV..CLR
Retrocopy LPPSLAMVSGQVFSAFMLCSTLLVIKMYVVAVITGQVRLPKKAFANPKDDLRQGDLQYCWSYSDVQFCLR

Parental  AHRNDMETIYPFLFLGLVYSFLGPHPVVAWAHFLIFLLGRLVHTWAY
          .H.ND.ETIY.F.FLGLVY.FLGP.P.......LIFLLG...HT.AY
Retrocopy THWNDVETIYLFFFLGLVYTFLGPDPFLHLNVLLIFLLGLVLHTVAY

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_953 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_953 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000004909	1 retrocopy	retro_itri_953 ,