RetrogeneDB ID: retro_opri_82

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2071:253713..254512(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000000096
• Aliases: None
• Description: None

Sequence

>retro_opri_82
GGAGTGAAGACTGGCCGCTGCCTGCGAGGAGGGAATTCAACCCAGGGCACCTGTGAGATCTTCACCTGGTGTCCAGTGGA
GACCAAGTCCGTGCCCAGGAAGCCATTGCTGGGGGATGCTGAAGACTTCACTGTTTATATAAAGAACTTCACCCGCTTCC
CCAAATTCAACTTCTCCAAGACGAACGTGGACACGGACAAGGCGCTGCTGAAATCCTGTCGCTTTGGCCCCAACAACCTC
TAGTGCCCCATCTTCCATGTATGCTCTGTGGCCCGCTGGGCGGGGAGCACCTGTGAGGACATAGCCCTGGAGGGCGGTGT
GATCAGCATTCACATTGATTGGAACTGTGATCTTGACCAACCAGGCTCTGAATGCAACCCTCACTACTCTTTGAGCCGTC
TGGACCACAACTTTACAAAGTCTATATCCTCAGGGTACCACTTCAGGTTTGCCAAGTACTACCGAGTTGCTGCGGGGAAG
GAGTTCCGCACCTTGATTAAAGCCTATGGCATCTGCTTTGATGTGCTGGTGAATGGGCAGGGCAGCTTTTGTCTGTGACC
TGGTGCTCATCAACATCATTAAGAAGAGAGAGTTCTACTGAGAGAAGAAGTTTGAGAAAGTGAGGGGCCAAGAGGACCGG
GCCCTGGAGGCTAAAGACCAGGTACAGGGGCAGGAGGAGTTGGAGCAGGAGTCGCTTGCCTCGGGGCTGATGGAACTACC
CAGGACACTGCGGAGCAGCAGCCAGGACGGTGGTTTTCAGGGGAACGGCAGTGTGTGCCGACAGGTGCTGGAGTCTGAC

Alignment

ORF - retro_opri_82 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.77 %
• Parental protein coverage: 72.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVKTGRCLPAGNSTQGTCEIFAWCPVETKSMPRKPLLGDAEDFTVYIKNFIRFPKFNFSKTNVDTDKTLL
          GVKTGRCL..GNSTQGTCEIF.WCPVETKS.PRKPLLGDAEDFTVYIKNF.RFPKFNFSKTNVDTDK.LL
Retrocopy GVKTGRCLRGGNSTQGTCEIFTWCPVETKSVPRKPLLGDAEDFTVYIKNFTRFPKFNFSKTNVDTDKALL

Parental  KSCHFGPNNLYCPIFHVGSVVRWAGSTFEDIALEGGVIGIHIEWDCDLDQPGSECNPHYSFSRLDHKFXX
          KSC.FGPNNL.CPIFHV.SV.RWAGST.EDIALEGGVI.IHI.W.CDLDQPGSECNPHYS.SRLDH.F..
Retrocopy KSCRFGPNNL*CPIFHVCSVARWAGSTCEDIALEGGVISIHIDWNCDLDQPGSECNPHYSLSRLDHNFTK

Parental  XXXXXXXXXFAKYYRDAAGMEFRTLIKAYGIRFDVLVN-GRAAFVCDLVLIYIIKKREFYREKKFEKVRG
          .........FAKYYR.AAG.EFRTLIKAYGI.FDVLVN.GRAAFVCDLVLI.IIKKREFY.EKKFEKVRG
Retrocopy SISSGYHFRFAKYYRVAAGKEFRTLIKAYGICFDVLVN>GRAAFVCDLVLINIIKKREFY*EKKFEKVRG

Parental  RDDRTLEAEDQVQGQEE----SLASGLMELPRT-PEQQQDGGFQGNGSVCRQVLESD
          ..DR.LEA.DQVQGQEE....SLASGLMELPRT.....QDGGFQGNGSVCRQVLESD
Retrocopy QEDRALEAKDQVQGQEELEQESLASGLMELPRTLRSSSQDGGFQGNGSVCRQVLESD

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_82 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000000096	2 retrocopies	retro_opri_668, retro_opri_82 ,