RetrogeneDB ID: retro_itri_401

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:80789..81281(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO27
• Ensembl ID: ENSSTOG00000027765
• Aliases: None
• Description: F-box protein 27 [Source:HGNC Symbol;Acc:18753]

Sequence

>retro_itri_401
CCTCCGGAAATGGATGGTGCAGCACAGTGGAAATGGCTGCGTGGTGGAAAAAAGAAAAAGAAAACCCGTGGGGGGGGGGG
AGCTACAGCTACACAAAACTGTTTCGTACTTCCTTCAGTTGGTGCTGCAAGAAGCAGGTCTTGGACCTGGAGGAGGAGGG
TCTATAGCCAGAACTGCTGGACAGAAGCAGGATTAAGATTTGTGTCTCTGACTGGTGGGGAGCCTGACACGACAGTGGCT
GTATGTATGGACTCCTTGTCCAACTTCTAGACACTGACCAGATCATCCTAGATAAATTCTCTGCTGTGCCTGACCCCCAT
TAAGCAGTGGAACAACAATATCTGTCTTCAAGTCACCCATGTGTTCTCCAACATCAAGACAGGTGTCCGTTTTGTGTCTT
TTGAACACTGGGGGCAGGACACGCAGTTCTGGGCTGGCCACTATGGAGCCCGTGTGACCAACTCCAGTGTGATCATACGG
GTCTCTCAGTCC

Alignment

ORF - retro_itri_401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.62 %
• Parental protein coverage: 58.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PCGQEGLRKWMVQHGGDGWVVEENRRTVPGAPSQTCFV-TSFRWCRKKQVLDLEEEGLWPELLDSGRIEI
          P....G...W....GG........R........Q.CFV.TSF.WC.KKQVLDLEEEGL.PELLD..RI.I
Retrocopy PPEMDGAAQWKWLRGGKK--KKKTRXXXXATATQNCFV<TSFSWCCKKQVLDLEEEGL*PELLDRSRIKI

Parental  CVSDWWGARHDCGCKYRLLVQLLDADQTILDTFSAVPDP-IEQWNNNICFQVTHVFSNIKTGVRFVSFEH
          CVSDWWGA.HD.GC.Y.LLVQLLD.DQ.ILD.FSAVPDP.I.QWNNNIC.QVTHVFSNIKTGVRFVSFEH
Retrocopy CVSDWWGA*HDSGCMYGLLVQLLDTDQIILDKFSAVPDP>IKQWNNNICLQVTHVFSNIKTGVRFVSFEH

Parental  WGQDTQFWAGHYGARVTNSSVILRVSQS
          WGQDTQFWAGHYGARVTNSSVI.RVSQS
Retrocopy WGQDTQFWAGHYGARVTNSSVIIRVSQS

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_401 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_401 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004611	1 retrocopy	retro_cpor_1475,
Mustela putorius furo	ENSMPUG00000017748	3 retrocopies	retro_mputfur_1473, retro_mputfur_465, retro_mputfur_965,
Ictidomys tridecemlineatus	ENSSTOG00000027765	1 retrocopy	retro_itri_401 ,
Tupaia belangeri	ENSTBEG00000010522	1 retrocopy	retro_tbel_1067,
Tursiops truncatus	ENSTTRG00000009850	1 retrocopy	retro_ttru_1161,
Vicugna pacos	ENSVPAG00000004974	1 retrocopy	retro_vpac_470,