RetrogeneDB ID: retro_opri_1098

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_70700:4208..4604(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB6B
• Ensembl ID: ENSOPRG00000001164
• Aliases: None
• Description: RAB6B, member RAS oncogene family [Source:HGNC Symbol;Acc:14902]

Sequence

>retro_opri_1098
TTCCATAGCCTCATTTCCACTTACTTACGCAATTCTGCTGCAGCCATAGTAGTTTATGATATTAAAAGTGTCAATTGCTT
CCAGCAAACTGCAAAATGGACTGACGATGTCAGAACAGAAAGAAAAAGTGGTGTTATCATCATGCTAGTACGAAATGAAA
CAGATGTTGTTGACAAGAAGCCAGTGTCTACTGAGGAAGGAGAGAGGAAAGCCAGAGCTGAATGTCATGTTTATTGAAAC
TAGTGAAAAAGCAGGATAAACATAAAGCAGCTTTTCTGATGTGTGGCAGCAGCTTTGCCTGGAATGGAAAGCACACAGGA
CAGAAGCAGAGAAGGCATGATTGACATAAAAGTGGAAAAGCCTCAGGACCAGCCAGTCGGCAAAGGCTGTTCCTGC

Alignment

ORF - retro_opri_1098 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.56 %
• Parental protein coverage: 64.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FRSLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVIIMLVGNKTD-LADKRQITIEEGEQ
          F.SLI..Y.R.S..A.VVYDI...N.FQQT.KW.DDVRTER.S.VIIMLV.N.TD.L....Q......E.
Retrocopy FHSLISTYLRNSAAAIVVYDIKSVNCFQQTAKWTDDVRTERKSGVIIMLVRNETD>LLTRSQCLLRK-ER

Parental  RAKELSVMFIETSAKTG-YNVKQLFRRVASALPGMENVQEKSKEGMIDIKLDKPQEPPASEGGCSC
          ...EL.VMFIETS.K.G..N.KQLF..VA.ALPGME..Q..S.EGMIDIK..KPQ..P....GCSC
Retrocopy GKPELNVMFIETSEKAG<INIKQLF*CVAAALPGMESTQDRSREGMIDIKVEKPQDQPVGK-GCSC

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_1098 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 6 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009412	1 retrocopy	retro_etel_1486,
Loxodonta africana	ENSLAFG00000009905	1 retrocopy	retro_lafr_430,
Ornithorhynchus anatinus	ENSOANG00000031623	1 retrocopy	retro_oana_94,
Ochotona princeps	ENSOPRG00000001164	5 retrocopies	retro_opri_1098 , retro_opri_20, retro_opri_606, retro_opri_797, retro_opri_993,
Ochotona princeps	ENSOPRG00000010355	6 retrocopies	retro_opri_1082, retro_opri_1085, retro_opri_1095, retro_opri_1118, retro_opri_247, retro_opri_858,
Pongo abelii	ENSPPYG00000003663	3 retrocopies	retro_pabe_2097, retro_pabe_2191, retro_pabe_3537,