RetrogeneDB ID: retro_opri_378

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_104040:6..666(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB21
• Ensembl ID: ENSOPRG00000011037
• Aliases: None
• Description: RAB21, member RAS oncogene family [Source:HGNC Symbol;Acc:18263]

Sequence

>retro_opri_378
GCAGCGGCTGGCTGGCAGTGACAGGTAGCAGCCGATGCCTACAGGTTCAACGTGGTGCTGCTGGAGGAAGCCTGCATGGC
AAAGACGTCGCTGGTGTTGCACTACTGAGAGAACAAGTTGAAGAACAAGCATATCACCACCATGCAGGCATCTTTTTAAA
ATAAGTTAACTATTGGTGGGAAAAGAGTAAATCTTGCCATTTGGGATACAGCAGGTCAAGAGAGTCCATGCATTGGGACC
AATTTACTACAGAGATTCAAAGGAGCTATTTTAGTTTATGATATAAAGGATGAAGATTCTTTTCAGAAGGTAAAAAAAAC
TGGATCAAAGAATTACAGAAAATGTTGGGAAATGAAATCTGTTCATATATAGTTGGTAATAAAATAGACTTGGAAAAGGA
GAGACATGTTTCCACTCAAGAAGCAGAATCACACGCACAATCTGTGGGAAAGAAACATCATCATACTTCAGCCAAACAAA
ACAAAGAAATTGAGGAATTCTGTCTTGACCTTTGTAAAAGGATAATAGAAACAGCACCGGTAGATGATGGGAGGGCAAAA
GACAGTGGTTCCAGCCAACCAGGAGCTGCACAACGAGGTATGCAGATTACTGATGATGAGCCTCAGGCTCAGCAGTGGAG
GAGGGTGCTGTTCTTCTGGA

Alignment

ORF - retro_opri_378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.0 %
• Parental protein coverage: 99.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAAGGA-AAAGRPYSFKVVLLGEGCVGKTSLVLRYCENKFNDKHITTLQASFLTKKLNIGGKRVNLAIWD
          AAAG.....A...Y.F.VVLL.E.C..KTSLVL.Y.ENK...KHITT.QASF...KL.IGGKRVNLAIWD
Retrocopy AAAGWQ*QVAADAYRFNVVLLEEACMAKTSLVLHY*ENKLKNKHITTMQASF-*NKLTIGGKRVNLAIWD

Parental  TAGQERFHALGPIYYRDSNGAILVYDITDEDSFQKVKNW-VKELRK-MLGNEICLCIVGSKIDL-KERHV
          TAGQE.....G........GAILVYDI.DEDSFQK......K..RK.MLGNEIC..IVG.KIDL.KERHV
Retrocopy TAGQES-PCIGTNLLQRFKGAILVYDIKDEDSFQKXXXXGSKNYRK<MLGNEICSYIVGNKIDLEKERHV

Parental  SILEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRMIETAQVDE-RAKGNGSSQPGAARRGVQIIDDE
          S..EAES.A.SVG.KH.HTSAKQNK.IEE..LDLCKR.IETA.VD..RAK..GSSQPGAA.RG.QI.DDE
Retrocopy STQEAESHAQSVGKKHHHTSAKQNKEIEEFCLDLCKRIIETAPVDDGRAKDSGSSQPGAAQRGMQITDDE

Parental  PQAQ-SSGGGCCSSG
          PQAQ.S.G.GCCSSG
Retrocopy PQAQ>SGG-GCCSSG

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_378 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004732	1 retrocopy	retro_dord_457,
Microcebus murinus	ENSMICG00000009168	1 retrocopy	retro_mmur_176,
Myotis lucifugus	ENSMLUG00000013239	1 retrocopy	retro_mluc_2070,
Ochotona princeps	ENSOPRG00000007883	3 retrocopies	retro_opri_1061, retro_opri_1116, retro_opri_299,
Ochotona princeps	ENSOPRG00000011037	1 retrocopy	retro_opri_378 ,