RetrogeneDB ID: retro_itri_1167

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393392.1:444243..444594(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000025724
• Aliases: None
• Description: None

Sequence

>retro_itri_1167
CTCCAGGGAGCTCTTCCCAGGACTTGTGGCAGGAGGCTGCTGAGCTAGCTGCATTTCACAGGCTCTGTGTTCTTAGCATA
GTCCATGATGTTTGTTATTAGCACTGTCAGTGGACATCTGGGCAAAATTGAGGGGAATGTTGTTATGCTTGCTGTTTTGG
TTGTGAATGCTGTTGGGATTTCCATTGAAACCAAATTAGCTTTGGCTTGTGACACACTAACGTGTCAATTCTTTGGAGAC
GTGAAATGCATGAGGATCATTCTTCAAAGAAGAACCCTCATTTTGATGTCGTGTGTTCTACCTTACTGGGCTATCCTCTT
CAATATGGAGGATATTCTCTAGCTCTTAAAA

Alignment

ORF - retro_itri_1167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.8 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRGALP-SDLRREALELAAL-AGPVFLAQLMIFLISIVSSIFCGHLGKVELDAVTLAVSVVNVTGISVGT
          L.GALP..DL..EA.ELAA...G.VFLA..M.F.IS.VS....GHLGK.E...V.LAV.VVN..GIS..T
Retrocopy LQGALP<QDLWQEAAELAAF>TGSVFLA*SMMFVISTVS----GHLGKIEGNVVMLAVLVVNAVGISIET

Parental  GLASACDTLMSQSFGGKNLKRVGIILQRGILILLLCCFPCWAIFINTENLLLLLK
          .LA.ACDTL..Q.FG....K...IILQR..LIL..C..P.WAI..N.E..L.LLK
Retrocopy KLALACDTLTCQFFG--DVKCMRIILQRRTLILMSCVLPYWAILFNMEDIL*LLK

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_1167 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1167 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000025724	1 retrocopy	retro_itri_1167 ,