RetrogeneDB ID: retro_itri_84

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393333.1:6098917..6099628(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000024760
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RIT1
• Ensembl ID: ENSSTOG00000021028
• Aliases: None
• Description: Ras-like without CAAX 1 [Source:HGNC Symbol;Acc:10023]

Sequence

>retro_itri_84
CCTGAAGGGTGGTTTTCCGTGGGGGGTCACCTGGGACTTCCCAAGAGGACAATGGCTTCTGGAACTCGCCCCGTTGGTGG
CTACCCTAGCAACCCTGCAGGGGTCACTCGAGAGTACAAATTAGTGATGCTGGGTGCTGGTGGTGTGGGGAAGAGCGCCA
TGACCATGCAGTTCGTCAGCCGCCAGTTCCCAGAAGATCATGACCCCACCATTGAAGACGGCTATAAAACACGGGTTCGT
GTTGATGACGAACCTGTCAATCTGGACATTGTGGATACAACGGGACAGGCAGAGTTTACAGCCCTGCGGAATCGCTACCT
GAGTGCAGGAGAAGGATTTATCATCTGTTACTCTGTCACAGATCGCCAAAGTTTCGATGCAGTTCGGGAGTTTAAAGAGC
TTATTGATCAAGTCGGACATACTAACGAAACACCTGTGGTTCTTGTCGGAAACAAGTCTGACCTAAAACAGCTAAGACAG
GTCACCAAGGAAGAAGGGTTAGCTCTGGCCCAGGAATTCAGCTGTCCATTTTTTGAGACCTCCGCTGCATACCGCTGCTA
CGTTGACAATGTCTTCCATACACTTGTACAGGAGATCCGAAGGAAAGAAAAGGAGGCAGAGCTGGACGTAAAGAAAAAAT
CCAAACCCAAAAGCAATATATGGAAGAAAATAAAATCCCCTTTCCAGAAGAACAAAGATTCGGTAGCTTGA

Alignment

ORF - retro_itri_84 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.73 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSGTRPVGSCCSNPAGLSREYKLVMLGAGGVGKSAMTMQFISHRFPEDHDPTIEDAYKIRIRIDDEPAN
          M.SGTRPVG...SNPAG..REYKLVMLGAGGVGKSAMTMQF.S..FPEDHDPTIED.YK.R.R.DDEP.N
Retrocopy MASGTRPVGGYPSNPAGVTREYKLVMLGAGGVGKSAMTMQFVSRQFPEDHDPTIEDGYKTRVRVDDEPVN

Parental  LDILDTAGQAEFTAMRDQYMRAGEGFIICYSITDRRSFHEVREFKQLIYRVRRTDDTPVVLVGNKSDLKQ
          LDI.DT.GQAEFTA.R..Y..AGEGFIICYS.TDR.SF..VREFK.LI..V..T..TPVVLVGNKSDLKQ
Retrocopy LDIVDTTGQAEFTALRNRYLSAGEGFIICYSVTDRQSFDAVREFKELIDQVGHTNETPVVLVGNKSDLKQ

Parental  LRQVTKEEGMALAREFSCPFFETSAAYRYYIDDVFHALVREIRKKEKEAVLAMEKKSKKTNCLWSRFKDQ
          LRQVTKEEG.ALA.EFSCPFFETSAAYR.Y.D.VFH.LV.EIR.KEKEA.L...KKSK.....W...K..
Retrocopy LRQVTKEEGLALAQEFSCPFFETSAAYRCYVDNVFHTLVQEIRRKEKEAELDVKKKSKPKSNIWKKIKSP

Parental  ISKLKDS
          ..K.KDS
Retrocopy FQKNKDS

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_84 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_84 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314, retro_itri_1315,
Ictidomys tridecemlineatus	ENSSTOG00000021028	1 retrocopy	retro_itri_84 ,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,