RetrogeneDB ID: retro_itri_423

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393290.1:12843572..12843947(-)
• Located in intron of: ENSSTOG00000019515

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACYP1
• Ensembl ID: ENSSTOG00000007327
• Aliases: None
• Description: acylphosphatase 1, erythrocyte (common) type [Source:HGNC Symbol;Acc:179]

Sequence

>retro_itri_423
GTGTGGCTGGGGGCAGTTGGCTTTGTGGTTGCTGGTGTGATTTGGCCCCTTGTGGGGAAAACTAAGAGGGTTTGAGGATG
GCAGAAGGGGACACCTTGGTATCAGTGGATTACAAAATTTTGAGGAAGGTGCAAGGGGTGGTTTTCCACAAGTACACTCA
GGCTGAGGGTAAAAAGCTAGGATTGGCAGGCTGGGTCCAGAAGACTGACCGGAGCACGGTGCAAGGACAATTGCAAGGTC
CTATCTTTAAGGTGCATCACATGCAGGAATGGCTTGAGACAACAGGAAGTCCCAAATCGCACATTGACAAAGCAAATTTC
AACCATGAGAAAAATCATCTTGAAATTTGATTACTCTGATTTTGAAATTGTGAAA

Alignment

ORF - retro_itri_423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 80.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VWLAGVGLLIA-FLSTLGCSARAPGLSMAEGDTLVSVDYEIFGKVQGVFFRKYTQAEGKKLGLVGWVQNT
          VWL..VG...A.......C.....GL.MAEGDTLVSVDY.I..KVQGV.F.KYTQAEGKKLGL.GWVQ.T
Retrocopy VWLGAVGFVVA<WCDLAPCGEN*EGLRMAEGDTLVSVDYKILRKVQGVVFHKYTQAEGKKLGLAGWVQKT

Parental  DRGTVQGQLQGPISKVRRMQEWLETKGSPKSHIDRANFSNE-KVILKLDYSEFQIVK
          DR.TVQGQLQGPI.KV..MQEWLET.GSPKSHID.ANF..E.K.ILK.DYS.F.IVK
Retrocopy DRSTVQGQLQGPIFKVHHMQEWLETTGSPKSHIDKANFNHE>KIILKFDYSDFEIVK

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_423 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_423 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000007327	1 retrocopy	retro_itri_423 ,
Drosophila melanogaster	FBgn0085190	1 retrocopy	retro_dmel_5,