RetrogeneDB ID: retro_opri_976

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_51704:3141..3619(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STYX
• Ensembl ID: ENSOPRG00000016123
• Aliases: None
• Description: serine/threonine/tyrosine interacting protein [Source:HGNC Symbol;Acc:11447]

Sequence

>retro_opri_976
CGACAGAATATGTAAGCCAAGCTTTATTATACCAAGTTTCAGCAGTTATTTAGGTATTTAGTCTGGGATATTGCAGATAA
TCCAGTGAAAATATAATACGTTATTTCCCCATGACTAAAGAATTTATGATGGGAGCTTACAAAGTGGAGGAAAAGTACTT
GTGCATGGAAATGCAGGGATCTCCAGAAGTGCTGCGTTTGTTATTGCATACATTATGGAAACATTTGGAGTGAAGTACAG
AGATGCAGTTACTTATGTTCAAGAAAGGAGGTTTTGTATTAATCCTAATGTTGGATTTGTGCATCAGCTTCAGCAATATG
AAGCCATCTACCTAGCAAAATTAATGATACAGATGATGTCACCGCTTCAGATGGAAAGATCAGTATCTGTTCATTCTGGA
ACCACAGGCAGTTTGAAGAGAACACATGAAGAAGATGATGACTTTGGAAACACGCAAGTGGCGACTGCACAGAATGGC

Alignment

ORF - retro_opri_976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 71.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RQNIEANFIKPNFQQLFRYLVLDIADNPV-ENIIRY-FPMXXXXXXXXXXXXXKVLVHGNAGISRSAAFV
          RQN..A......FQQLFRYLV.DIADNPV.ENIIRY.FP..............KVLVHGNAGISRSAAFV
Retrocopy RQNM*AKLYYTKFQQLFRYLVWDIADNPV<ENIIRY<FPHD*RIYDGSLQSGGKVLVHGNAGISRSAAFV

Parental  IAYIMETFGMKYRDAFTYVQERRFCINPNVGFVHQLQEYEAIYLAKLTIQMMSPLQIERSLSVHSGTTGS
          IAYIMETFG.KYRDA.TYVQERRFCINPNVGFVHQLQ.YEAIYLAKL.IQMMSPLQ.ERS.SVHSGTTGS
Retrocopy IAYIMETFGVKYRDAVTYVQERRFCINPNVGFVHQLQQYEAIYLAKLMIQMMSPLQMERSVSVHSGTTGS

Parental  LKRTHVEDDDFGNMQVATAQNG
          LKRTH.EDDDFGN.QVATAQNG
Retrocopy LKRTHEEDDDFGNTQVATAQNG

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_976 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 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016631	9 retrocopies	retro_dnov_1713, retro_dnov_1720, retro_dnov_1914, retro_dnov_2138, retro_dnov_2186, retro_dnov_2218, retro_dnov_2221, retro_dnov_461, retro_dnov_66,
Echinops telfairi	ENSETEG00000000561	1 retrocopy	retro_etel_1881,
Monodelphis domestica	ENSMODG00000029372	1 retrocopy	retro_mdom_44,
Mus musculus	ENSMUSG00000053205	1 retrocopy	retro_mmus_96,
Oryctolagus cuniculus	ENSOCUG00000029442	1 retrocopy	retro_ocun_1555,
Ochotona princeps	ENSOPRG00000016123	1 retrocopy	retro_opri_976 ,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365,
Vicugna pacos	ENSVPAG00000012229	1 retrocopy	retro_vpac_464,