RetrogeneDB ID: retro_opri_608

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_19189:7180..7507(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000003353
• Aliases: None
• Description: None

Sequence

>retro_opri_608
TCTGGGGCCAACAGTCCCGTCAAGGAATGCTTCACCCTGTGTGCTCTGGGGACCCGAGAGCATTGGGATGCTGTCTACAA
GAAAGAATTACAGACAATCCGGGAATGTGGGGATACAGGAGAGATCTGGTTTGGAGAAGAGAGCATGACTCGACTGATGA
GGTGGATGCAGACACAGAAGGTTCCATTGGATGCCTCAGTGCTGGCTATTGGAAATGGAACTGATGTTTTTTTGGTTGAA
CTTGCAAAATTTGATTTCAGTAATATTACTGGAATTGATTACTCTCCCTCAGCATTTCAACTTTCTGGAAGCATCCTAGA
GAAAGAA

Alignment

ORF - retro_opri_608 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.45 %
• Parental protein coverage: 52.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGARSPAEDGFAPSALGTREHWDAVYERELQTFQECGDTGEIWFGEESMTRLLRWMQKRKVPLDASVLDI
          .GA.SP....F...ALGTREHWDAVY..ELQT..ECGDTGEIWFGEESMTRL.RWMQ..KVPLDASVL.I
Retrocopy SGANSPVKECFTLCALGTREHWDAVYKKELQTIRECGDTGEIWFGEESMTRLMRWMQTQKVPLDASVLAI

Parental  GTGNGVFLVELXAKFGFHNITGI-YSPSAIQ-SGNILEKE
          G.G..VFLVEL.AKF.F.NITGI.YSPSA.Q.SG.ILEKE
Retrocopy GNGTDVFLVEL-AKFDFSNITGIDYSPSAFQLSGSILEKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_608 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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
Oryctolagus cuniculus	ENSOCUG00000004774	1 retrocopy	retro_ocun_1889,
Ochotona princeps	ENSOPRG00000003353	1 retrocopy	retro_opri_608 ,