RetrogeneDB ID: retro_opri_478

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_13435:40039..40632(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CALB2
• Ensembl ID: ENSOPRG00000012294
• Aliases: None
• Description: calbindin 2 [Source:HGNC Symbol;Acc:1435]

Sequence

>retro_opri_478
GAAATGAAAACTTTTGTGGATCAGTATGGGCAGAGAGATGATGGAAAAATAGGAATTGTAGAGTTGGCCCATGTATTACC
CACGGAAGAGAATTTCCTGCTGCTATTCCAGTGCCAGCAGCTGAAGTCCTGTGAGGATTTCATGAAGACATGGAGAAAAT
ATGATACTGATCACAGTGGCTTCATAGAAACTGAGGAGCTGAAGAACTTTCTAAAGGACCTGCTGGAGAAGGCAAACAAC
ACTGTTGATGACACAAAATTAGATGAATATACAGACCTAATGCTGAAACTATTTGATTCAAATAATGATGGGAAGCTGGA
ATTAACCGAGATGGCAAGGTTACTACCAGTGCAAGAGAATTTCCTTCTTAAATTTCAGGGAATCAAAATGTGTGGGAAAG
AGTTCAATAAGGCTTTTGAGTTATATGATCAGGATGGCAATGGATACATAGATGAAAATGAACTGGAAGCTTTGCTAAAG
GACCTGTGTGAGAAGAATAAACAGGAACTGGATATTATAATATTCCAACATACAAGAAGAACATAATGGCTTTGTTGGAT
GGAGGGAAGCTCTACCGAACAGATCTTGCCTTA

Alignment

ORF - retro_opri_478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.3 %
• Parental protein coverage: 82.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMKEFMQKYDKNSDGKIEMAELAQILPTEESFLLCFR-QCVGSSAEFMEAWRKYDTDRSGYIEANELKGF
          .MK.F...Y....DGKI...ELA..LPTEE.FLL.F..Q...S...FM..WRKYDTD.SG.IE..ELK.F
Retrocopy EMKTFVDQYGQRDDGKIGIVELAHVLPTEENFLLLFQCQQLKSCEDFMKTWRKYDTDHSGFIETEELKNF

Parental  LSDLLKKANRPYDEAKLQEYTHTILRMFDLNGDGKLGLSEMSRLLPVQENFLLKFQGMKLTSEEFNAIFT
          L.DLL.KAN...D..KL.EYT...L..FD.N.DGKL.L.EM.RLLPVQENFLLKFQG.K....EFN..F.
Retrocopy LKDLLEKANNTVDDTKLDEYTDLMLKLFDSNNDGKLELTEMARLLPVQENFLLKFQGIKMCGKEFNKAFE

Parental  FYDKDGSGYIDENELDALLKDLYEKNKKEMNI-QQLTSYRKSVMSLAEAGKLYRKDLEI
          .YD.DG.GYIDENEL.ALLKDL.EKNK.E..I......Y.K..M.L...GKLYR.DL..
Retrocopy LYDQDGNGYIDENELEALLKDLCEKNKQELDI<YNIPTYKKNIMALLDGGKLYRTDLAL

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_478 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	ENSOPRG00000012294	1 retrocopy	retro_opri_478 ,