RetrogeneDB ID: retro_opri_1118

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_72662:2197..2609(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB6C
• Ensembl ID: ENSOPRG00000010355
• Aliases: None
• Description: RAB6C, member RAS oncogene family [Source:HGNC Symbol;Acc:16525]

Sequence

>retro_opri_1118
TCAGAAACAATGTATTTGGAGGATAGAAAAGCCAGGCTAATGTGTGGAATGCTGTGGATCAGGCACATGTTCATAGCCTC
ATTCCCAGTGACATCCTTGATTCTTTTGCAAGTATAGTAGTTCACAATATTACAAATGTTAATGGCTTCCAGCAAACTCC
AAAATGGGTTGATAATATCAGAACAGAAAGAGGAAATGATGATATCATCGTGCTAGCACAAATTAAAACAGATCTTGTTG
ACAAGAAGCAAGTGTCTACTGAGGAGGGAAAGAGGAAAGCCAATGAGCTAAATGCCATGTTTATTGAAACTAGTGAGAAA
GCAAAATAAATGTAAAGAAGCTCTTCTGACTTGTGGCAACAGCTTTGCCTGGAATAGAAAACACACAGGACAGAATGAGG
AAAGATATGATT

Alignment

ORF - retro_opri_1118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 73.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKTMYLEDRTIRLQ-LWDTAGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVI
          S.TMYLEDR..RL...W....Q....SLIPS.I.DS.A..VV..ITNVN.FQQT.KW.D..RTERG.D.I
Retrocopy SETMYLEDRKARLM<VWNAVDQAHVHSLIPSDILDSFASIVVHNITNVNGFQQTPKWVDNIRTERGNDDI

Parental  IMLVGNKTDLADKRQVSIEEGERKAKELNVMFIETSAKA-GYNVKQLFRRVAAALPGMESTQDRSREDMI
          I.L...KTDL.DK.QVS.EEG.RKA.ELN.MFIETS.KA...NVK.LF..VA.ALPG.E.TQDR.R.DMI
Retrocopy IVLAQIKTDLVDKKQVSTEEGKRKANELNAMFIETSEKA<KINVKKLF*LVATALPGIENTQDRMRKDMI

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_1118 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000175582	1 retrocopy	retro_hsap_7,
Nomascus leucogenys	ENSNLEG00000017098	1 retrocopy	retro_nleu_200,
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,
Ictidomys tridecemlineatus	ENSSTOG00000023497	3 retrocopies	retro_itri_1743, retro_itri_1827, retro_itri_1885,