RetrogeneDB ID: retro_itri_1491

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393507.1:2152188..2152552(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000020783
• Aliases: None
• Description: None

Sequence

>retro_itri_1491
CCACCCAAAGATGACACGAAGAAAGATGCCAGAAAGTCGGCAAGAAAGACAAGGACCCCCAGTGAACAAATCTGGAAGCA
AACCAAAAAAGAAGAATTGGTCCAAAGGCAAAGTTCAGGACAAGCTCAATAATCTAGTCTTGACAAAGCTTCTTATGTCA
AACTCTGTAAGGAAGTTCCCAACTATAAGCTTATAAGACCCAGCTGTGGTCTCTGAGAGACAGAAGATTCGAGGTTTCCT
GGCCAGGGAAGCTGAAATGCTCCTCAGCAAAGGGCTTATCAAACTGGTTTCAAAGCACAGAGCTCAAGTAATTTATACCA
AAAATACCAAGGGTAGAGATGCCCCAGCTGTTGGTGAAGATGCA

Alignment

ORF - retro_itri_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPKDDKKKKDAGKSAKKDKDP-VNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITP
          PPKDD.KK.DA.KSA.K...P.VNKSG.K.KKK.WSKGKV.DKLNNLVL..K..........P...L..P
Retrocopy PPKDDTKK-DARKSARKTRTP>VNKSGSKPKKKNWSKGKVQDKLNNLVL-TKLLMSNSVRKFPTISL*DP

Parental  AVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA
          AVVSER.KIRG.LAR.A...LLSKGLIKLVSKHRAQVIYT.NTKG.DAPA.GEDA
Retrocopy AVVSERQKIRGFLAREA-EMLLSKGLIKLVSKHRAQVIYTKNTKGRDAPAVGEDA

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_1491 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1491 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 9 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012395	3 retrocopies	retro_cfam_500, retro_cfam_680, retro_cfam_984,
Felis catus	ENSFCAG00000001151	3 retrocopies	retro_fcat_1792, retro_fcat_601, retro_fcat_903,
Latimeria chalumnae	ENSLACG00000017531	4 retrocopies	retro_lcha_101, retro_lcha_118, retro_lcha_50, retro_lcha_72,
Macropus eugenii	ENSMEUG00000014185	3 retrocopies	retro_meug_1181, retro_meug_1562, retro_meug_174,
Microcebus murinus	ENSMICG00000002687	8 retrocopies	retro_mmur_1023, retro_mmur_1514, retro_mmur_229, retro_mmur_308, retro_mmur_387, retro_mmur_425, retro_mmur_485, retro_mmur_688,
Macaca mulatta	ENSMMUG00000016894	2 retrocopies	retro_mmul_137, retro_mmul_71,
Ochotona princeps	ENSOPRG00000016194	9 retrocopies	retro_opri_1099, retro_opri_1204, retro_opri_256, retro_opri_320, retro_opri_393, retro_opri_493, retro_opri_64, retro_opri_854, retro_opri_873,
Ictidomys tridecemlineatus	ENSSTOG00000020783	3 retrocopies	retro_itri_1491 , retro_itri_196, retro_itri_87,
Vicugna pacos	ENSVPAG00000000266	4 retrocopies	retro_vpac_106, retro_vpac_118, retro_vpac_337, retro_vpac_546,