RetrogeneDB ID: retro_opri_387

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_10527:75913..76528(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSN2
• Ensembl ID: ENSOPRG00000013114
• Aliases: None
• Description: casein beta [Source:HGNC Symbol;Acc:2447]

Sequence

>retro_opri_387
GAAACTATTATGATGCATTCTACTATAAAATTATCATGAAAAGCCATGAATGAAAAAGTTGAATCATGGACTCATGATTC
TTCTCCTTCTTTCCAGGAGAAACTCCAGGAAAAAATCCTCCCCTTTATTCAGTCACAGCCTCTGCTCTATCCTTATGCTG
AGCCCATCCCTTTCCCTGCTCCGCCACAGAACACCCTGAACCTTGTCCAACCTGACATGCTGCTCCCTCTCCTCCAGCCT
GAAATAATGGAAGATCCCAAAGCTAAGGAGGCCACCTTTCCTAAGCGCAAAGTGATGCCCTTCCTCAAATCCCCAATGGC
TTTCCCCTTTGTTGACCCTCAACTCCTGAGTCTCAGGGAGCTGAAAACTCAGCACCCTTTTCTGCCCGAGCTCCTGCCCT
TCATGCACCAGTTCTTCCAACCTTTTTTCCAGACTCCCATGCTTTATCCTCAGACCCAGTTGCCTGTTCCTCAGACCAAA
TTTGTGCCCATTCCCCAACAAATGGTACCCTACACCCAAAGAGACATGCCTGTCGAAGCCCTTCAACTGTTCCAAGACCT
GCGCTTCCCTACCCATGGGTTCTACCCTGTGGCTCAGCCACTTGCCCCAGTTAAT

Alignment

ORF - retro_opri_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.83 %
• Parental protein coverage: 92.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETLESVSTSEETITQYKQKLEKVKHEEQLQREEKLQEKILPFIQSQPLLYPYAEPIPFPAPPQNTLNLVQ
          ET....ST..........K.E...H.......EKLQEKILPFIQSQPLLYPYAEPIPFPAPPQNTLNLVQ
Retrocopy ETIMMHSTIKLS*KAMNEKVESWTHDSSPSFQEKLQEKILPFIQSQPLLYPYAEPIPFPAPPQNTLNLVQ

Parental  PDMLLPLLQPEIMEDPKAKEATFPKRKVMPFLKSPMAFPFVDPQLLSLRELKTQHPFLPELLPFMHQFFQ
          PDMLLPLLQPEIMEDPKAKEATFPKRKVMPFLKSPMAFPFVDPQLLSLRELKTQHPFLPELLPFMHQFFQ
Retrocopy PDMLLPLLQPEIMEDPKAKEATFPKRKVMPFLKSPMAFPFVDPQLLSLRELKTQHPFLPELLPFMHQFFQ

Parental  PFFQTPMLYPQTQLPVPQTKFVPIPQQMVPYTQRDMPVEALQLFQDL-LPTHGFYPVAQPLAPVN
          PFFQTPMLYPQTQLPVPQTKFVPIPQQMVPYTQRDMPVEALQLFQDL..PTHGFYPVAQPLAPVN
Retrocopy PFFQTPMLYPQTQLPVPQTKFVPIPQQMVPYTQRDMPVEALQLFQDLRFPTHGFYPVAQPLAPVN

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_387 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	ENSOPRG00000013114	1 retrocopy	retro_opri_387 ,