RetrogeneDB ID: retro_opri_20

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1032:246595..247061(+)
• 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_20
TCAGAGACAATGTTTTTGGAGGATAGAAAAGCCAGGCTAATGTGTGGAATGCTGTGGATCAGGCACATGTTCATAGCCTC
ATTCCCAGTGACATCCTTGATTCTTTTGCAAGTATAGTAGTTCACAATATTACAAATGTTAATGGCTTCCAGCAAACTCC
AAAATGGGTTGATAATATCAGAACAGAAAGAGGAAATGATGATATCATCATGCTAGCACAAATTAAAACAGATCTTGTTG
ACAAGAAGCAAGTTTCTACTGAGGAGAGAAAGAGAAAAGCCAATGAGCTAAATGCCATGTTTATTGAAACTAGTGAGAAA
GCAAAATAAATGTAAAGAAGCTCTTCTGACTTGTGGCAACAGCTTTGCCTGGAATAGAAAACACACAGGACAGAATGAGG
AAAGATATGATTAACATAAACCTGGAAAAGCCTCAGGTCCAGCCAGTCAGCAAATGCTGTTCCTGC

Alignment

ORF - retro_opri_20 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.72 %
• Parental protein coverage: 75.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKTMYLEDRTVRLQ-LWDTAGQERFRSLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVI
          S.TM.LEDR..RL...W....Q....SLIPS.I.DS....VV..ITN.N.FQQT.KW.D..RTERG.D.I
Retrocopy SETMFLEDRKARLM<VWNAVDQAHVHSLIPSDILDSFASIVVHNITNVNGFQQTPKWVDNIRTERGNDDI

Parental  IMLVGNKTDLADKRQITIEEGEQRAKELSVMFIETSAK-TGYNVKQLFRRVASALPGMENVQEKSKEGMI
          IML...KTDL.DK.Q...EE....A.EL..MFIETS.K....NVK.LF..VA.ALPG.EN.Q......MI
Retrocopy IMLAQIKTDLVDKKQVSTEERKRKANELNAMFIETSEK<SKINVKKLF*LVATALPGIENTQDRMRKDMI

Parental  DIKLDKPQEPPASEGGCSC
          .I.L.KPQ..P.S...CSC
Retrocopy NINLEKPQVQPVSK-CCSC

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_20 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,