RetrogeneDB ID: retro_itri_1096

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393374.1:6416628..6416876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTS
• Ensembl ID: ENSSTOG00000013277
• Aliases: None
• Description: 6-pyruvoyltetrahydropterin synthase [Source:HGNC Symbol;Acc:9689]

Sequence

>retro_itri_1096
ATTGATCCTGTTACAAATATGAATTTGAATTTGACAGACCTCTTAAATATACGAAGTAGACAATTATGAAGTCCTTTGAT
CTAAGAATCTGGATATGGATGTGTTGTACTTTGTGGATATTCTAAGTATGACAATAAATGTGGCTGTATATACCTGAGAA
AAACCTCTAGAAATTCCTTCTGACGGGAGTTCTTTATAAAGTAAAAGTATATGAAACTGACAAAAATATTGTAGTCTATG
AAGGAGAA

Alignment

ORF - retro_itri_1096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.28 %
• Parental protein coverage: 69.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IDPVTGMVMNLTDLK-KYMEEAIMKPLD-HKNLDLDVPYFADVVSTTENVAVYIWE-NLQKFLPVGVLYK
          IDPVT.M..NLTDL..KY....IMK..D..KNLD.DV.YF.D..S.T.NVAVY..E.NL.KFL..GVLYK
Retrocopy IDPVTNMNLNLTDLL<KYTK*TIMKSFD<SKNLDMDVLYFVDILSMTINVAVYT*E>NL*KFLLTGVLYK

Parental  VKVHETDNNIVVYKGE
          VKV.ETD.NIVVY.GE
Retrocopy VKVYETDKNIVVYEGE

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_1096 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1096 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000013	2 retrocopies	retro_chof_1925, retro_chof_2556,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Ictidomys tridecemlineatus	ENSSTOG00000013277	1 retrocopy	retro_itri_1096 ,