RetrogeneDB ID: retro_itri_1458

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393493.1:133219..133449(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRFIP2
• Ensembl ID: ENSSTOG00000023775
• Aliases: None
• Description: leucine rich repeat (in FLII) interacting protein 2 [Source:HGNC Symbol;Acc:6703]

Sequence

>retro_itri_1458
CTGGATGAAAAACCTGACAAACTGTAGGCTGAAAATGACACAAGGCCTTCAAGTTGAAACTCTGCTTTGGCAGCAAATCT
CTAAGTGGAAACTCATCCAGATGAGGAAGTGGTGACACCAACAGCTTCATAGATCCAGACACCTCATTAACTGAATTACC
ATAGTGTTTGAAGCACAGGAAAAAATCCAAAAAAGGTATAGTTTTCAGTGAACATTTAAATCAAGAAGAA

Alignment

ORF - retro_itri_1458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.49 %
• Parental protein coverage: 54.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDEKSDKQYAENYTRPSSRNSASATT-PLSGNSSRRGSGDTSSLIDPDTSLSELRESLSEVEEKYKKAMV
          LDEK.DK..AEN.TRPSS.NSA.A....LSGNSSR.GSGDT.S.IDPDTSL.EL...L.....K.KK..V
Retrocopy LDEKPDKL*AENDTRPSS*NSALAAN<SLSGNSSR*GSGDTNSFIDPDTSLTELP*CLKH-RKKSKKGIV

Parental  SNAQLDNEK
          ....L..E.
Retrocopy FSEHLNQEE

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_1458 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1458 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
Macaca mulatta	ENSMMUG00000022539	1 retrocopy	retro_mmul_2595,
Ictidomys tridecemlineatus	ENSSTOG00000023775	1 retrocopy	retro_itri_1458 ,