RetrogeneDB ID: retro_opri_247

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4219:134831..135224(-)
• Located in intron of: ENSOPRG00000007337

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_247
ATGTTCCTGGGGGAGTAGAGCATTGGAAAGACATTCTTGATCACCAGATTCATGTATGGTATTTTTGACAACACCTACCA
GGAAAAAAACTGGCATTGATTTTTTTAAATCAAAAACAATGTGTTTGGAGGATTGAGTAATCAGGGTATGGTGTGGGATA
CTGTTGATCAGGAATGTTTCCATAGCCTCGTTTCCACTTACATCCGCACTTCTGCTGCAGCCATAATAGTTTATGATATT
ACAAGTGTCAATTGCTTCCAGCAAACTACAAAATGGATTGACAATATCAGAACAGAAAGAAGAAGTGGTGTTATCATCAT
GCTAGTACGAAATGAAACAGATGTTGTTGACAAGAAGCAAGTGTCTACTGAGGAAGGAGAGAGGAAAGCCAGA

Alignment

ORF - retro_opri_247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 68.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFLGEQSVGKTSLITRFMYDSFDNTYQAT-IGIDFL-SKTMYLEDRTIRL-QLWDTAGQERFRSLIPSYI
          .FLGE.S.GKT.LITRFMY..FDNTYQ....GIDF..SKTM.LED..IR....WDT..QE.F.SL...YI
Retrocopy MFLGE*SIGKTFLITRFMYGIFDNTYQEK>TGIDFFKSKTMCLED*VIRV<MVWDTVDQECFHSLVSTYI

Parental  RDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEEGERKAK
          R.SAAA..VYDIT.VN.FQQTTKWID..RTER.S.VIIMLV.N.TD..DK.QVS.EEGERKA.
Retrocopy RTSAAAIIVYDITSVNCFQQTTKWIDNIRTERRSGVIIMLVRNETDVVDKKQVSTEEGERKAR

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_247 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,