RetrogeneDB ID: retro_itri_1534

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393533.1:528152..528728(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAF
• Ensembl ID: ENSSTOG00000026759
• Aliases: None
• Description: OAF homolog (Drosophila) [Source:HGNC Symbol;Acc:28752]

Sequence

>retro_itri_1534
ATTCACACCTTCCGCGCCCTGATCCTGGGGGAACTGGAAAAGGGGCAGAGTCAATTCCAGGCCCTCTGTTTTGTCACCCT
ACTGCACCACAGTGAGATCATCCCCAGTGAGGCCATGGCCAAGCTGCGGCAGAAAAACCCACGGGCAGTGAGGCAGGCTG
AGGAGATGCAGGGCCTGGAACAGCTGCACATGGACATCGCTGTGAAGTTCAGCCAGGATGGCCTGCTGAGTCCCCATCTT
CACAACGCATGCGCTGAGGCCGCAGATGCCTTTTACACCTACCAGGAGAATGTCCAGTTCTGGCTGGAACAAGATGTGGA
CAGCTTTGTCTTAGAGGCTCTACCTAAGGCATCTGAGCAGATGGAACTGCCTCGCTGCAGGCTGGTGGGGGACCATAGGA
AGCCCTGCACCTGCTGCCATGGCCTGAGCCTAGCCTAATACCCCTGCAAGCTCAAGTACTACCACAGCTGTGAGCAGCCC
ACGCCCTACAAGTGTGGCATCCGAAGCTGCCAGAAGAACTACAGCTTTGACTTCTCTGTGCCCCAGAGGCAACTGTGTCT
TTGGGATGAGGACCCC

Alignment

ORF - retro_itri_1534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.9 %
• Parental protein coverage: 74.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKIFRALILGELEKGQSQFQALCFVTRLHHNEIIPSEAMAKLRQKNPRAVRQAEEMRGLEQLHMDIAVNF
          ...FRALILGELEKGQSQFQALCFVT.LHH.EIIPSEAMAKLRQKNPRAVRQAEEM.GLEQLHMDIAV.F
Retrocopy IHTFRALILGELEKGQSQFQALCFVTLLHHSEIIPSEAMAKLRQKNPRAVRQAEEMQGLEQLHMDIAVKF

Parental  SQGGLLSPHLHNVCAEAADAIYTRQEDVRFWLEQGVDSSVFEALPKASEQMELPRCRQVGDREKPCTCRY
          SQ.GLLSPHLHN.CAEAADA.YT.QE.V.FWLEQ.VDS.V.EALPKASEQMELPRCR.VGD..KPCTC..
Retrocopy SQDGLLSPHLHNACAEAADAFYTYQENVQFWLEQDVDSFVLEALPKASEQMELPRCRLVGDHRKPCTCCH

Parental  GLSLAWYPCMLKYCHSRERPAPYKCGIRSCQKNYNFDFYVPQRQLCLWDEDP
          GLSLA.YPC.LKY.HS.E.P.PYKCGIRSCQKNY.FDF.VPQRQLCLWDEDP
Retrocopy GLSLA*YPCKLKYYHSCEQPTPYKCGIRSCQKNYSFDFSVPQRQLCLWDEDP

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_1534 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1534 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	ENSSTOG00000026759	1 retrocopy	retro_itri_1534 ,