RetrogeneDB ID: retro_itri_814

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393327.1:879432..879972(+)
• Located in intron of: ENSSTOG00000021864

Retrocopy information

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

Parental gene information

• Parental gene symbol: EPS15L1
• Ensembl ID: ENSSTOG00000020658
• Aliases: None
• Description: epidermal growth factor receptor pathway substrate 15-like 1 [Source:HGNC Symbol;Acc:24634]

Sequence

>retro_itri_814
CTATATGAAAAATACTATAGACAGGTCGATACAGGCAATACTGGAAGGTTGTGGGCTTCAGATGCTGCTGCTTTTCTGAA
AAAGTCAGGGCTTCTAGACTTGATATTTGGAAAGATTTGGGATTTAGCTGACACAGATGGCAAAGGCATCCTGAGCAAAC
AAGAATTCTTTGTGATTTTGCATCTTGTAGCGTGTGCCCAGAATGGACTGGAGGTTTCACTGAATTGCTTGAACTTGGCT
CTTCCTCCACCAAGATTTCATGATACCAGTAGTCCTTTACTAACCAGTGAACCCCTGCAGCTGAGCTTCCATGGGCTGTT
AAAAGTGAAGATAAGGCCAAATATGATGCAATTTTTGATAGTTTAAGTCCAGTGAATGGATTTTTGTCTGGTGATAAGGT
GAAGCCAGTGTTACTCAACTCTTAAGTTACCTGTGGAAATCCTTAGAAGAGTTTGGGAGTTGAGTGATATTGACCATGGT
GGAAAGCTTGACAGAGATGAGTTTGCAGTTGTAAATAACTTAATGTTCTTAAAATATGAA

Alignment

ORF - retro_itri_814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.74 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LYESYYKQVDPAYTGRVGASEAALFLKKSGLSDIILGKIWDLADPEGKGFLDKQGFYVALRLVACAQSGH
          LYE.YY.QVD...TGR..AS.AA.FLKKSGL.D.I.GKIWDLAD..GKG.L.KQ.F.V.L.LVACAQ.G.
Retrocopy LYEKYYRQVDTGNTGRLWASDAAAFLKKSGLLDLIFGKIWDLADTDGKGILSKQEFFVILHLVACAQNGL

Parental  EVTLSNLSLSMPPPKFHD-TSSPLMVTP-PSAEAPWAVRVEEKAKFDGIFESLLPINGLLSGDKVKPVLM
          EV.L..L.L..PPP.FHD..S..L...P.P.AE.PWAV..E.KAK.D.IF.SL.P.NG.LSGDKVKPVL.
Retrocopy EVSLNCLNLALPPPRFHDTSSPLLTSEP<PAAELPWAVKSEDKAKYDAIFDSLSPVNGFLSGDKVKPVLL

Parental  NS-KLPLDVLGRVWDLSDIDKDGQLDRDEFAVAMHLVYRALE
          NS.KLP...L.RVW.LSDID..G.LDRDEFAV...L.....E
Retrocopy NS>KLPVEILRRVWELSDIDHGGKLDRDEFAVVNNLMFLKYE

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_814 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_814 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013985	1 retrocopy	retro_cjac_1122,
Ictidomys tridecemlineatus	ENSSTOG00000020658	2 retrocopies	retro_itri_1831, retro_itri_814 ,