RetrogeneDB ID: retro_itri_1831

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393956.1:133369..133994(+)
• Located in intron of: None

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_1831
CAGTTATCAAGTGGGAATCCTGTATAAGAAAAATACTATAGACAGGTTGATACAGGCAATACTGGAAGGGTGCTGGCTTC
AGATGCTGCTGCTTTTCTGAAAAAGTCAGGGCTTCCAGACTTGATACTTGGAAAGATTTCGGATTTAGCTGACACAGATG
CAAAGGCATCCTGAACAAACAAGAATTCTTTGTGGCTTTGCATCTTGTAGCATGTGCCCAGAATGGATTGGAGGTTTCAC
TGAATAGCTTGACTTGGCTGTTCCTCTACCAAGATTTCATGATACCATTAGTCCTTTACTAACCAGCGGAACCCCTGCAG
CTGAGCTTCCATGGGCTTTTAAAAGTGAAGATAAAGCCAAATATGATGTAATTTTTGATAGTTTAAGTCCAGTGGATGGA
TTTTTGTCTGGTGATAAAGTGAATCCAGTGTTGCTCAACTCTAAGTTACCTGTGGAAATCCTTGGAAGAGTTTGGGAATT
GAGTGATATTGACCATGATGGAAAGCTTGACAGAGATGAGCTTGCAGTTGCCATGTTTTTGGTATACTCTGTATTGGAGA
AGGAACCCGTGCCAATGGCCTTGCTTCCAGCCTTGTTGCCACCTTCTAAGAGAAAAACGTGGGTT

Alignment

ORF - retro_itri_1831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.93 %
• Parental protein coverage: 67.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QIPTGNPLYESYYKQVDPAYTGRVGASEAALFLKKSGLSDIILGKIWDLADPEGK-GFLDKQGFYVALRL
          Q...GNP..E.YY.QVD...TGRV.AS.AA.FLKKSGL.D.ILGKI.DLAD...K.G.L.KQ.F.VAL.L
Retrocopy QLSSGNPV*EKYYRQVDTGNTGRVLASDAAAFLKKSGLPDLILGKISDLADTDAK<GILNKQEFFVALHL

Parental  VACAQSGHEVTLSNLS-LSMPPPKFHDTSSPLMVT-PPSAEAPWAVRVEEKAKFDGIFESLLPINGLLSG
          VACAQ.G.EV.L..L..L..P.P.FHDT.SPL.....P.AE.PWA...E.KAK.D.IF.SL.P..G.LSG
Retrocopy VACAQNGLEVSLNSLT<LAVPLPRFHDTISPLLTSGTPAAELPWAFKSEDKAKYDVIFDSLSPVDGFLSG

Parental  DKVKPVLMNSKLPLDVLGRVWDLSDIDKDGQLDRDEFAVAMHLVYRALEKEPVPSVLPPSLIPPSKRKKT
          DKV.PVL.NSKLP...LGRVW.LSDID.DG.LDRDE.AVAM.LVY..LEKEPVP..L.P.L.PPSKRK..
Retrocopy DKVNPVLLNSKLPVEILGRVWELSDIDHDGKLDRDELAVAMFLVYSVLEKEPVPMALLPALLPPSKRKTW

Parental  V
          V
Retrocopy V

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_1831 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1831 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,