RetrogeneDB ID: retro_itri_1755

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393719.1:366707..367297(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO3
• Ensembl ID: ENSSTOG00000016405
• Aliases: None
• Description: F-box protein 3 [Source:HGNC Symbol;Acc:13582]

Sequence

>retro_itri_1755
TTTGGCATATATACTGGCTTGAGTCAGTACATAACAGTGGAAGCAGTGCAGGGTGAAACAAAAATGAAGTTTTCTACCAA
TGTCCAGACAAAATGAATCAGAATCCAACTGCTATTGACATGTTTATCATAGGTGCTACTTTTACTGACTGATTTAGCTT
TTATGTCAAAAATGTTGTATCAGGTGGCTTTCTCCATCATCAGAAACCAAATTTTCAGATATGTTCACGATCCAGAGTGC
ATGGCAACACCTAGGGATATTATAGTGTCAGTTTCCACATCATTTCTGCCAGAAAGCAGCTCTGTACATCCACCCCACTA
TTTCTTCACATACCGCATCAGGATTGAAATGTCAAAGGATGCACTTCCTGAGAAAGCATGTCAGTTGGACAGTTGCTAAT
GGAGAATAACAAATGCTAAGGGTGATGTAGAAGAAGTTCAAGGACCGAGAGTAGTTGGTGAATTTCCTATCATCAGCCCA
GGTCGGGCACATGAGTACACCAGCTGTACCCATTCTCTACATCATCAGGATATACGGAAGGATATTATACCTTCCATTTT
CTTTATTTTAAAGACAAGATCTTTAAAATG

Alignment

ORF - retro_itri_1755 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83. %
• Parental protein coverage: 55.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FCIHTGLSQYIAVEAAEGR-NKNEVFYQCPDQMARNPAAIDMFIIGATFTDWFTSYVNNVVSGGF-PIIR
          F.I.TGLSQYI.VEA..G..NKNEVFYQCPD.M..NP.AIDMFIIGATFTD.F..YV.NVVSGGF..IIR
Retrocopy FGIYTGLSQYITVEAVQGE<NKNEVFYQCPDKMNQNPTAIDMFIIGATFTD*FSFYVKNVVSGGF>SIIR

Parental  DQIFRYVHDPECVATTGDITVSVSTSFLPELSSVHPPHYFFTYRIRIEMSKDALPEKACQLDSRYWRITN
          .QIFRYVHDPEC.AT..DI.VSVSTSFLPE.SSVHPPHYFFTYRIRIEMSKDALPEKACQLDS..WRITN
Retrocopy NQIFRYVHDPECMATPRDIIVSVSTSFLPESSSVHPPHYFFTYRIRIEMSKDALPEKACQLDSC*WRITN

Parental  AKGDVEEVQGPGVVGEFPIISPGRVYEYTSCT-TFSTTSGYMEGYYTFHFLYFKDKIFNV
          AKGDVEEVQGP.VVGEFPIISPGR..EYTSCT..FST.SGY.EGYYTFHFLYFKDKIF..
Retrocopy AKGDVEEVQGPRVVGEFPIISPGRAHEYTSCT<PFSTSSGYTEGYYTFHFLYFKDKIFKM

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_1755 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1755 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
Macropus eugenii	ENSMEUG00000006623	2 retrocopies	retro_meug_1744, retro_meug_857,
Ictidomys tridecemlineatus	ENSSTOG00000016405	1 retrocopy	retro_itri_1755 ,