RetrogeneDB ID: retro_opri_605

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_19141:4228..4582(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000004911
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000009190
• Aliases: None
• Description: None

Sequence

>retro_opri_605
AGTAGAGGCCTAAGTGACCAGGATAGTGGCCAGGGATACAACCTGTATCTAATCGGTTACTTGGACAAGCAGTGTCAGAT
ACCCGTATGCAGGAGACAGACTGGATCCTGGTGGAGAAGTGCTGCTGGGACATTGCCTTGGATCCCCGAAGCAGACTCCC
AAGAACCTCTTCATCACGTATATGGCAGGCAATACTATCTCCAATACCCTACCATGATGGTGTGCATGATGGCCTGGCAA
TCGATTCAGGCAATCATGGCTATCTCAGCCCACTTTCAAGATGCTAGAAAGTTCAAGCCAGAAACTTCTACAGGGTTTGG
TCTATCTTATTGGGAACCTAATGGGTCTGGCATT

Alignment

ORF - retro_opri_605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.92 %
• Parental protein coverage: 68.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRGRSDRGSGQGDNLYPVGYLDKQ-VPDTSVQETDRILVEKRCWDIALGPL-KQIPMNLFIMYMAGNTIS
          SRG.SD..SGQG.NLY..GYLDKQ.V.DT..QETD.ILVEK.CWDIAL.P..KQ.P.NLFI.YMAGNTIS
Retrocopy SRGLSDQDSGQGYNLYLIGYLDKQ<VSDTRMQETDWILVEKCCWDIALDPR<KQTPKNLFITYMAGNTIS

Parental  -IFPTMMVCMMAWRPFKMLESSSQKFLQGLVYLIGNLMGLALAVYKCQSMGL
          ...PTMMVCMMAW.........S..F............G..L........G.
Retrocopy <QYPTMMVCMMAWQSIQAIMAISAHFQDARKFKPETSTGFGLSYWEPNGSGI

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_605 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005576	2 retrocopies	retro_chof_1859, retro_chof_254,
Dipodomys ordii	ENSDORG00000008407	2 retrocopies	retro_dord_387, retro_dord_581,
Echinops telfairi	ENSETEG00000001688	1 retrocopy	retro_etel_1631,
Felis catus	ENSFCAG00000001736	1 retrocopy	retro_fcat_759,
Macropus eugenii	ENSMEUG00000004615	1 retrocopy	retro_meug_1129,
Microcebus murinus	ENSMICG00000003864	2 retrocopies	retro_mmur_1313, retro_mmur_180,
Oryctolagus cuniculus	ENSOCUG00000006160	4 retrocopies	retro_ocun_1686, retro_ocun_395, retro_ocun_719, retro_ocun_817,
Ochotona princeps	ENSOPRG00000009190	1 retrocopy	retro_opri_605 ,
Pteropus vampyrus	ENSPVAG00000003824	1 retrocopy	retro_pvam_386,
Rattus norvegicus	ENSRNOG00000005719	1 retrocopy	retro_rnor_897,
Ictidomys tridecemlineatus	ENSSTOG00000000516	1 retrocopy	retro_itri_1008,