RetrogeneDB ID: retro_opri_751

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_28053:31127..32123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF39
• Ensembl ID: ENSOPRG00000011104
• Aliases: None
• Description: PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20314]

Sequence

>retro_opri_751
ATTAAAAGACCTTATTTTCATGTGAAACCATTGGAAAAGGCACAGCTTAAAAACTGGAAAGAATATTTAGAATTTGAAAT
TGAAAACGGGACTCATGAACGAGTTGTGGTTCTCTTTGAAAGATGTGTCATATCATGTGCCCTCTATGAGGAGTTTTAGA
TTAAGTATGCCTAGTACATGGAAAACCATAGCATTGAAGGAGTGAGGCATGTCTTCAGCAGAGCTTGTACTATTCATCTT
CCAAAGAAACCCATGGTGCATATGCTTTGGGCAGCTTTTGAGGAGCAACAGGGCAATATTAATGAAGCCAAGAATATCTT
AAGAACATTTGAAGAATGTATTCTAGGACTGGCAAAGGTTCGTTTGCGAAGAGTAAGTTTAGAACGTCGGCATGGAAATA
TGGAAGAAGCTGAGCATTTGCTTCAGGATGCCATTAAAAATGCCAAATCAAGTAATGAGTCATCCTTTTATGCTATCAAA
CTAGCCCGGCATCTTTTCAAAATACAAAAAAATCTTCCAAAGTCAAGGAAGGTGTTTTTAGAAGCCATTGAAAGAGACAA
AGAGAACACAAAGTTATACCTCAATTTACTTGAAATGGAATATAGTGGTGACCTCAAATAAAATGAAGAAAATATCCTCA
GTTATTTTGACAAAGCTGTACATGGATCATTACCTATTAAAATGAGAATTACATTCTCTCAAAGAAAAGTGGAATTTCTT
GAAGATTTTGGTTCAGATGTTAATAAGCTTCTGAATGCTTATGACGAACATCAAACACTCCTAAAAGAACAGGATTCCTT
AAAAAGGAAAGCAGAAAATGGATCAGAAGAACCAGAGGAGAAGAAAGCACATACGGATGACACAACCTCATCATCTACAC
AGATGATTGACGGTGATTTACAGGCAAATCAAGCTGCATATAATTATAGTGCCTGGTATCAATACAATTATCAGAATCCT
TGGAATTATGGACAGCATTATCCTCCCCCTCCGACG

Alignment

ORF - retro_opri_751 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.29 %
• Parental protein coverage: 60.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IKRPYFHVKPLEKAQLKNWKEYLEFEIENGTHERVVVLFERCVISCALYEEFWIKYAKYMENHSIEGVRH
          IKRPYFHVKPLEKAQLKNWKEYLEFEIENGTHERVVVLFERCVISCALYEEF.IKYA.YMENHSIEGVRH
Retrocopy IKRPYFHVKPLEKAQLKNWKEYLEFEIENGTHERVVVLFERCVISCALYEEF*IKYA*YMENHSIEGVRH

Parental  VFSRACTIHLPKKPMVHMLWAAFEEQQGNINEARNILRTFEECVLGLAMVRLRRVSLERRHGNMEEAEHL
          VFSRACTIHLPKKPMVHMLWAAFEEQQGNINEA.NILRTFEEC.LGLA.VRLRRVSLERRHGNMEEAEHL
Retrocopy VFSRACTIHLPKKPMVHMLWAAFEEQQGNINEAKNILRTFEECILGLAKVRLRRVSLERRHGNMEEAEHL

Parental  LQDAIKNAKSSNESSFYAIKLARHLFKIQKNLPKSRKVLLEAIERDKENTKLYLNLLEMEYSGDLKQNEE
          LQDAIKNAKSSNESSFYAIKLARHLFKIQKNLPKSRKV.LEAIERDKENTKLYLNLLEMEYSGDLK.NEE
Retrocopy LQDAIKNAKSSNESSFYAIKLARHLFKIQKNLPKSRKVFLEAIERDKENTKLYLNLLEMEYSGDLK*NEE

Parental  NILSCFDKAVHGSLPIKMRITFSQRKVEFLEDFGSDVNKLLNAYDEHQTLLKEQDSLKRKAENGSEEPEE
          NILS.FDKAVHGSLPIKMRITFSQRKVEFLEDFGSDVNKLLNAYDEHQTLLKEQDSLKRKAENGSEEPEE
Retrocopy NILSYFDKAVHGSLPIKMRITFSQRKVEFLEDFGSDVNKLLNAYDEHQTLLKEQDSLKRKAENGSEEPEE

Parental  KKAHTDDTTSSSTQMIDGDLQANQAAYNYSAWYQYNYQNPWNYGQYYPPPPT
          KKAHTDDTTSSSTQMIDGDLQANQAAYNYSAWYQYNYQNPWNYGQ.YPPPPT
Retrocopy KKAHTDDTTSSSTQMIDGDLQANQAAYNYSAWYQYNYQNPWNYGQHYPPPPT

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_751 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000011104	1 retrocopy	retro_opri_751 ,