RetrogeneDB ID: retro_itri_1503

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393515.1:16512..16835(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC1
• Ensembl ID: ENSSTOG00000006784
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) [Source:HGNC Symbol;Acc:9801]

Sequence

>retro_itri_1503
TTAATTTGCTTGTCCCATTTGAGTTCTGCATCATTTGAAAACATCCATGCAAAATGGCATTCCAAAGAGTGAAACCATTG
TCCATGTACTACCATAAACCTAATAAAAACTAAACTTGATCTGAAAGATGAAAATGACATTAAGAAACTGAAGGAGAAGA
AACTAACTTGTATCACATGTCCAATAGGGAGTGTTAAAGAGATCAAGGCTGTGGAATCCTAAGAGTGTTTAGGGCAATGA
AGTCTCAGGATAGTGTTTTATGAAGTTATTCCAGCATTTCTCTATTTACTCCCACCAAAAAGAGAGAGAACAAATCTCTT
CTG

Alignment

ORF - retro_itri_1503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.39 %
• Parental protein coverage: 56.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKE
          LIC.S..S.ASFEN..AKW......HCP.T.I.L..TKLDL.D..D.I.KLKEKKLT.IT.P.G....KE
Retrocopy LICLSHLSSASFENIHAKWHSKE*NHCPCTTINLIKTKLDLKDEND-IKKLKEKKLTCITCPIG--SVKE

Parental  IGAVKYLECSALTQRGLKTVFDEAIRAVLCPPP-VKKRKRKCLL
          I.AV...EC..L.Q..L..VF.E.I.A.L...P..KKR..K.LL
Retrocopy IKAVES*EC--LGQ*SLRIVFYEVIPAFLYLLP<TKKRENKSLL

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_1503 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1503 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 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000136238	6 retrocopies	retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Mus musculus	ENSMUSG00000001847	2 retrocopies	retro_mmus_1372, retro_mmus_234,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230,
Ictidomys tridecemlineatus	ENSSTOG00000000805	4 retrocopies	retro_itri_1158, retro_itri_1602, retro_itri_1615, retro_itri_431,
Ictidomys tridecemlineatus	ENSSTOG00000006784	1 retrocopy	retro_itri_1503 ,
Ictidomys tridecemlineatus	ENSSTOG00000023766	1 retrocopy	retro_itri_510,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Tarsius syrichta	ENSTSYG00000001618	2 retrocopies	retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,