RetrogeneDB ID: retro_itri_1447

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393490.1:2655512..2655859(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SIKE1
• Ensembl ID: ENSSTOG00000001684
• Aliases: None
• Description: suppressor of IKBKE 1 [Source:HGNC Symbol;Acc:26119]

Sequence

>retro_itri_1447
ATCCGGCAAGCAAACAGACAAATCAGAGAATTGCATCAAGAGAACAAAGAATTACGTACGTCCCTGGAAAAACATCAGTC
TGCATTGGAACTCATAATGAGCAAGTATCGAGAACAAATGTTTAGATTGCTCATGGCTAGCAAAAAAAAGATGATCCAGG
TATAATAATGAAGTTAAAGGAACAGCATTCCAAGGAGTTATAAGCACATGTTGACCAGACAATTGAAATGGCAGCAGTGA
TGAGGAAAGCCATTGAAATTGAGGAGCAACAGGGTTGCAAGGAGCAGGAACGAATATTTCAACTTGAACAAGAAAACAAG
GGCCTGAGAGAGATCCTTCAAATAACT

Alignment

ORF - retro_itri_1447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.43 %
• Parental protein coverage: 55.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSQENTQIRDLQQENRELWVSLEEHQDALELIMSKYRKQMLQ-LMVAKKAV-DAEPVLKAHQSHSAEIES
          ..Q.N.QIR.L.QEN.EL..SLE.HQ.ALELIMSKYR.QM...LM.......D.....K....HS.E...
Retrocopy IRQANRQIRELHQENKELRTSLEKHQSALELIMSKYREQMFRLLMASXXXM<DPGIIMKLKEQHSKEL*A

Parental  QIDRICEMGEVMRKAVQVDDDQFCKIQEKLAQLELENKELRELLSIS
          ..D...EM..VMRKA......Q.CK.QE...QLE.ENK.LRE.L.I.
Retrocopy HVDQTIEMAAVMRKAIEIEEQQGCKEQERIFQLEQENKGLREILQIT

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_1447 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1447 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012958	1 retrocopy	retro_chof_48,
Echinops telfairi	ENSETEG00000007805	1 retrocopy	retro_etel_615,
Loxodonta africana	ENSLAFG00000010502	1 retrocopy	retro_lafr_565,
Microcebus murinus	ENSMICG00000015446	1 retrocopy	retro_mmur_738,
Otolemur garnettii	ENSOGAG00000005952	2 retrocopies	retro_ogar_1794, retro_ogar_2028,
Ictidomys tridecemlineatus	ENSSTOG00000001684	1 retrocopy	retro_itri_1447 ,
Tupaia belangeri	ENSTBEG00000007772	1 retrocopy	retro_tbel_2455,