RetrogeneDB ID: retro_itri_292

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393282.1:10892980..10893294(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000028389
• Aliases: None
• Description: None

Sequence

>retro_itri_292
GCACACAAGTGTCCTACCTTATTTTTTGGCACCTGTGAAACTGCATTTTTAGGCCCTAAAGAACTTTTTCCATATAAAGA
AGCAAAGACATGTTTGGAAAGTCAAACACATGGAAATGAGTTAATGGATTGTGGGAAATAGACAGTAACCCAGGAGTGAA
ATGTACTGGAATCCAAGCAGCTCAGCAGCAGGGCTCTTCAGAAACCGAGGGAGAAGGTGGGCCTGCCACAGATGTGGGCA
GCGAGGGTGAGAGAGAAGCTGGAGAGGGCAGCCCAAGAGTGGAGAAGCCATGCGCTTCAGGGAAGTCCTCTAGG

Alignment

ORF - retro_itri_292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.81 %
• Parental protein coverage: 60.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ANKYPIFFFGTHETAFLGPKDLFPYKEYK-DKFGKSNKRKGFNEGLWEIENNPGVKFTGYQAIQQQSSSE
          A.K.P..FFGT.ETAFLGPK.LFPYKE.K.D.FGKSN..K..N.GLWEI..NPGVK.TG.QA.QQQ.SSE
Retrocopy AHKCPTLFFGTCETAFLGPKELFPYKEAK<DMFGKSNTWK*VN-GLWEIDSNPGVKCTGIQAAQQQGSSE

Parental  TEGEGGNTADASSEEEGDRVEEDGKGKRKNEKGGSKR
          TEGEGG...D..SE.E....E...........G.S.R
Retrocopy TEGEGGPATDVGSEGEREAGEGSPRVEKPCASGKSSR

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_292 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_292 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018527	1 retrocopy	retro_btau_1740,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Dasypus novemcinctus	ENSDNOG00000003696	2 retrocopies	retro_dnov_619, retro_dnov_819,
Echinops telfairi	ENSETEG00000010466	1 retrocopy	retro_etel_1234,
Loxodonta africana	ENSLAFG00000002512	1 retrocopy	retro_lafr_676,
Ictidomys tridecemlineatus	ENSSTOG00000028389	2 retrocopies	retro_itri_292 , retro_itri_864,
Tursiops truncatus	ENSTTRG00000004950	1 retrocopy	retro_ttru_1471,
Vicugna pacos	ENSVPAG00000004599	1 retrocopy	retro_vpac_380,