RetrogeneDB ID: retro_opri_1

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_47677:238..853(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000004467
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARHGDIB
• Ensembl ID: ENSOPRG00000015100
• Aliases: None
• Description: Rho GDP dissociation inhibitor (GDI) beta [Source:HGNC Symbol;Acc:679]

Sequence

>retro_opri_1
ATGGCCGAGCAGGAGTCCACGGCCGAGCAGCTGGCGCAGATCGCCGCCGAGAACGAGGAGGACGAGCACTCGGTCAACTA
CAAGCCGCCGGCGCAGAAGAGCATCCAGGAGATCCAGGAGCTGGACAAGGACGACGAGAGCCTGCGCAAGTACAAGGAGG
CGCTGCTGGGCCGCGTGGCCGTGTCGGCCGACCCCAGCGTGCCCAACGTGGTGGTGACGCGCCTCACGCTCTTGTGCAGC
TCGGCGCCCGGGCCCCTGGAGCTGGACCTGACGGGTGACCTGGAGAGCTTCAAGAAGCAGTCCTTTGTGCTGAAGGAGGG
CGTGGAGTACCGGATAAAGATCTCCTTCCGGGTGAACCACGAGATCGTGTCAGGCATGAAGTACATCCAGCACACCTACC
GGAAGGGCGTCAAGATCGACAAGACCGACTACATGGTGGGGAACTATGGGCCCCGCGCCGAGGAGTATGAGTTCCTGACG
CCCATGGAGGAGGCACCCAAGGGCATGCTGGCACGCGGCAGTTACAGCATCAAGTCCCGCTTCACCGATGATGACAAGAC
GGACCACCTGTCCTGGGAGTGGAACCTCACCATCAAGAAGGAGTGGAAGGACTGA

Alignment

ORF - retro_opri_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.1 %
• Parental protein coverage: 96. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVVEDDDELDSKLNYKPPPQKSLKELQEMDKDDESLTKYKKTLLGDGPVVADPTAPNVTVTRLTLVCESA
          Q......E.....NYKPP.QKS..E.QE.DKDDESL.KYK..LLG...V.ADP..PNV.VTRLTL.C.SA
Retrocopy QIAAENEEDEHSVNYKPPAQKSIQEIQELDKDDESLRKYKEALLGRVAVSADPSVPNVVVTRLTLLCSSA

Parental  PGPITMDLTGDLEALKKKVFVLKEGAEYRVKINFKXXXXXXXGLKYVQHTYRTGMKVDKVTFMVGSYGPR
          PGP...DLTGDLE..KK..FVLKEG.EYR.KI.F........G.KY.QHTYR.G.K.DK...MVG.YGPR
Retrocopy PGPLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNHEIVSGMKYIQHTYRKGVKIDKTDYMVGNYGPR

Parental  PEEYEFLTPIEEAPKGMLARGTYHTKSFFTDDDKQDHLTWEWNLSIKKDWTE
          .EEYEFLTP.EEAPKGMLARG.Y..KS.FTDDDK.DHL.WEWNL.IKK.W..
Retrocopy AEEYEFLTPMEEAPKGMLARGSYSIKSRFTDDDKTDHLSWEWNLTIKKEWKD

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_1 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	ENSOPRG00000015100	1 retrocopy	retro_opri_1 ,