RetrogeneDB ID: retro_itri_517

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393298.1:3930634..3931370(+)
• Located in intron of: ENSSTOG00000014581

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTG2
• Ensembl ID: ENSSTOG00000024521
• Aliases: None
• Description: mitochondrial ribosome-associated GTPase 2 [Source:HGNC Symbol;Acc:16239]

Sequence

>retro_itri_517
GTGCCTGCTGGCACCTTGGTGAAGGAGGGCAATGAGGTCATAGCCTACTTGTCCCAGCCAGGCCGGGAGTACATTGATGC
ACTGGGTGGGGAGGTGGGAAAAGCAACCACTTTTTCCTGGTTAATGACAGCTGTGCCCCTGTGACTTGCACCTCTGAACA
GCTGGGTCAGGAATGTATTCTTTACCTGGAGCTCGAGTCGGTGGGCCACTCCGGGATGGTCAGCTTCACCAGTGCTGGGA
AGCCCTCGCTCCTCCAGTCCATTTCAAATGTGAAAGCTGAAGTGGCTTCCTACCACTTCACCATTTTAAACCCCTATGTG
GGGATTGTTCACTACAAAGGTCAGCAATAGGTAGTGGCAGGTATCCTGGGCATCATCCAAGGTGCCCACCAGGACAGGGG
TCTTGGACTCAGCTTTCTCAGGCACATGGATCACTGCTGCTTCCTGTTGTTCATTGTGGACCTTTCCCTACCAGAGCCAT
GGACTCAGGTGAAGGGTTTAAAATACAAACTGGAGAAGAAGGCCTGTCTGAGAGGCCCCATGTGGTTGTTACAAACAAGA
TTGACCTTCCCCAGGCCAGAGCCCGTTTGCCCCAGCTCCAGGAACACCTGGGACAGGTCATCCTCTTGTCAGCAATGACT
GGGGAGAACCTGGGGCAGCTGCTGCTGCACCTGAAGGTGCTACATGATGCCTACCTGCAGGCCAAGCTCCTACGGAGCCA
CCAGCCACTCAGATGG

Alignment

ORF - retro_itri_517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.74 %
• Parental protein coverage: 61.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VPVGTLVKEGSEVVADLSQRGQEYIAALGG-AGGKGNRFFLANDNRAPVTCTPGEPGQERVLHLELKTVA
          VP.GTLVKEG.EV.A.LSQ.G.EYI.ALGG..GGK.N.FFL.ND..APVTCT....GQE..L.LEL..V.
Retrocopy VPAGTLVKEGNEVIAYLSQPGREYIDALGG<GGGKSNHFFLVNDSCAPVTCTSEQLGQECILYLELESVG

Parental  HAGMVGFPNAGKSSLLRAISNAKPAVASYPFTTLKPHVGIVHYEGHQQVAVADIPGIIRGAHQDKGLGLS
          H.GMV.F..AGK.SLL..ISN.K..VASY.FT.L.P.VGIVHY.G.QQ..VA.I.GII.GAHQD.GLGLS
Retrocopy HSGMVSFTSAGKPSLLQSISNVKAEVASYHFTILNPYVGIVHYKG-QQ*VVAGILGIIQGAHQDRGLGLS

Parental  FLRHIERCRFLLFIVDLSLPEPWTQVEDLKYELEKYEEGLSERPHVVVANKIDLPQ-ARAHLPQLQDHLG
          FLRH...C.FLLFIVDLSLPEPWTQV..LKY.LEK........P..........P..ARA.LPQLQ.HLG
Retrocopy FLRHMDHCCFLLFIVDLSLPEPWTQVKGLKYKLEK--KACLRGPMWLLQTRLTFPR<ARARLPQLQEHLG

Parental  QVIALSAVTGENLEQLLLHLQVLHRAYVEAELKRGSQPLRW
          QVI.LSA.TGENL.QLLLHL.VLH.AY..A.L.R..QPLRW
Retrocopy QVILLSAMTGENLGQLLLHLKVLHDAYLQAKLLRSHQPLRW

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_517 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_517 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000002751	1 retrocopy	retro_meug_138,
Ictidomys tridecemlineatus	ENSSTOG00000024521	1 retrocopy	retro_itri_517 ,