RetrogeneDB ID: retro_itri_1461

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393493.1:3126463..3126961(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C3orf52
• Ensembl ID: ENSSTOG00000001310
• Aliases: None
• Description: chromosome 3 open reading frame 52 [Source:HGNC Symbol;Acc:26255]

Sequence

>retro_itri_1461
AGTCCCTGGAGCTCCTGCAATAAGAAGTTGGTCGGTAAGTGTGAACTGTGGATGGTCATCACCTGCATCTTCCTGGGTCT
CATTATAGTGATCATCATTGGTTTATGTCTTAGTGGAGTAACTTATATTGATGAAGATGAAAATGAAATATTTGAGATAT
CATCAAACAAAACATTCTTCATCATGGTCAAGATTCCAGAAGAGTGCATTACAGAAGAGGAATTGCCTCACCTGCTTACT
AAAAGGCTTGAAGATGTGTACAGTAAATCTCCATCTCTGAGTCATTATTTCACTTCAGTTGAAATAGTGAACTTCAGTGG
TGAAAACGCCACAGCAACCTATCACCTGCAGTTTGCGGTTCCATGGGGAGATGACGGCTTTATGAAGTACATGATAAGTG
AGGAGCTTGCACTGGGAGTTTTGCTACAGGATTTCTATGATCAGAGTGTACCTCATTGTGAGAGTCTGGGGCTTGATCCA
GCATCTCTCTTGCTCTAT

Alignment

ORF - retro_itri_1461 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.98 %
• Parental protein coverage: 76.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPWSSCNKKLVGKCKLWMVITSIFLGLILVIIIGLCLSGVTYIDEDENEIFEISSNKTFFIMLKIPEECI
          SPWSSCNKKLVGKC.LWMVIT.IFLGLI.VIIIGLCLSGVTYIDEDENEIFEISSNKTFFIM.KIPEECI
Retrocopy SPWSSCNKKLVGKCELWMVITCIFLGLIIVIIIGLCLSGVTYIDEDENEIFEISSNKTFFIMVKIPEECI

Parental  TEEELPHLLTKRLEDVYSKSPSLSRYFTSVEIVDFSGENATATYHLQFGVPWEDDGFMKYMMSEELVLGV
          TEEELPHLLTKRLEDVYSKSPSLS.YFTSVEIV.FSGENATATYHLQF.VPW.DDGFMKYM.SEEL.LGV
Retrocopy TEEELPHLLTKRLEDVYSKSPSLSHYFTSVEIVNFSGENATATYHLQFAVPWGDDGFMKYMISEELALGV

Parental  LLQDFYDQSVPHCESLGLDPASLLLY
          LLQDFYDQSVPHCESLGLDPASLLLY
Retrocopy LLQDFYDQSVPHCESLGLDPASLLLY

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_1461 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1461 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	ENSSTOG00000001310	1 retrocopy	retro_itri_1461 ,