RetrogeneDB ID: retro_opri_847

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_3655:133742..134199(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA2
• Ensembl ID: ENSOPRG00000007086
• Aliases: None
• Description: pyrophosphatase (inorganic) 2 [Source:HGNC Symbol;Acc:28883]

Sequence

>retro_opri_847
CCTCAGACTCGGGAAGACCCGGGACACAATGATAAACATACGGCTGTTGTGGCGGCAATGACCCAATTCATGTGTGTGAA
ACTGGAAGTAAGGAGTGTGCAAGAGGTGAAATGATCAAGGTGAAAGTTCTGGACATATTGGCTATGATTGACGAAGGGGA
AAGCGACCGGAAAGTCATTGCTATTAATGAGGACGATCCTGATGTGACCAATTACAATGATATTAATGATGTCAAACGGC
AGACACCTGGCTACCTAGAAGCTACTGTGGACTGGTTTAGAAGGTACAAGGTTCCTGATGGAAAACCAGAAAATGAATTT
GCTTTCAATGCGGAATCTAAAGATAAGGACTTTGCAGTTAGTATTATTAAAAGCACTCGTGGCTGTTGGAAAGTTGTAGT
ACTAAGAAGATGGGTGGAGAGGGAATCAGCTGCACGAATACGACAGTGGCGGAAAGC

Alignment

ORF - retro_opri_847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.65 %
• Parental protein coverage: 51.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PQTWEDPGQTDEST-NCCGDNDPIDVCEIGSKVLTRGEVIPVKILGILALIDESETDWKLIAINANDPDA
          PQT.EDPG..D..T..CCG.NDPI.VCE.GSK...RGE.I.VK.L.ILA.IDE.E.D.K.IAIN..DPD.
Retrocopy PQTREDPGHNDKHT<GCCGGNDPIHVCETGSKECARGEMIKVKVLDILAMIDEGESDRKVIAINEDDPDV

Parental  SKFDDIDDVKKFKPGYLEATLNWFRYYKVPDGKPENQFAFNGEFRNKAFALEIIKSTHDHWKALLM-KKC
          ....DI.DVK...PGYLEAT..WFR.YKVPDGKPEN.FAFN.E...K.FA..IIKST...WK.....KK.
Retrocopy TNYNDINDVKRQTPGYLEATVDWFRRYKVPDGKPENEFAFNAESKDKDFAVSIIKSTRGCWKVVVL<KKM

Parental  DGGAINCTNVQVCDS
          .G..I.CTN..V..S
Retrocopy GGEGISCTNTTVAES

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_847 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
Canis familiaris	ENSCAFG00000010887	1 retrocopy	retro_cfam_405,
Choloepus hoffmanni	ENSCHOG00000008731	3 retrocopies	retro_chof_1052, retro_chof_430, retro_chof_769,
Echinops telfairi	ENSETEG00000014816	1 retrocopy	retro_etel_1959,
Macaca mulatta	ENSMMUG00000017004	1 retrocopy	retro_mmul_1278,
Monodelphis domestica	ENSMODG00000020635	5 retrocopies	retro_mdom_638, retro_mdom_795, retro_mdom_945, retro_mdom_946, retro_mdom_947,
Oryctolagus cuniculus	ENSOCUG00000005941	2 retrocopies	retro_ocun_1338, retro_ocun_1470,
Ochotona princeps	ENSOPRG00000007086	1 retrocopy	retro_opri_847 ,
Sus scrofa	ENSSSCG00000022365	1 retrocopy	retro_sscr_557,
Tursiops truncatus	ENSTTRG00000003141	2 retrocopies	retro_ttru_1307, retro_ttru_606,