RetrogeneDB ID: retro_opri_875

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_3973:98834..99309(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1A
• Ensembl ID: ENSOPRG00000003999
• Aliases: None
• Description: RAP1A, member of RAS oncogene family [Source:HGNC Symbol;Acc:9855]

Sequence

>retro_opri_875
TCTGTACAGTTCGTTCCAGGAATTTTTGTTGAAAAGTAGGATGCTACGATAGAAGATTCTTACAGAAAGCAAGTTGAACT
AGATGCACAATGGTGTGTGCTTGAAATCTTGGATACTGCACAAACGGAACAGCTCACAGCCAAGAGGGATTTGTACATGA
AGAATGGACAAGGCTTGGCATTGGTTTATTCCATCACCGCACAGTCCACATTGAACGATTTAGAAGATCTAAGAACAGAT
TCCTCGAGCTGAAGACACCGGTGAGGTTCCAATGATCCTAGCCGGTAATAAGCGTGATTTGGAAGATGAAAGAGTTGCAA
GTAAGGAGAAAAGTCAACATCTAGCCAGACGGCAAAATAACTGTGCATTCTTAAAATCTTCTGCAAAATCAAAAATAAAT
GTTAATGAGATCCTTCATGACCTAATGCGGCAAATTAACAGAAAAACCCCAATGGCCGCAAAGGCCCGCAAAAAG

Alignment

ORF - retro_opri_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.29 %
• Parental protein coverage: 96.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TVQFVQGIFVEKYDPTIEDSYRKQVEVDCQQCMLEILDTAGTEQFTAMRDLYMKNGPGFALVYSITAQST
          .VQFV.GIFVEK.D.TIEDSYRKQVE.D.Q.C.LEILDTA.TEQ.TA.RDLYMKNG.G.ALVYSITAQST
Retrocopy SVQFVPGIFVEK*DATIEDSYRKQVELDAQWCVLEILDTAQTEQLTAKRDLYMKNGQGLALVYSITAQST

Parental  FNDLQDLR-EQILRVK-DTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEI
          .NDL.DLR....L..K.DT..VPMIL.GNK.DLEDERV..KE..Q.LAR...NCAFL.SSAKSKINVNEI
Retrocopy LNDLEDLR<NRFLELK<DTGEVPMILAGNKRDLEDERVASKEKSQHLARRQNNCAFLKSSAKSKINVNEI

Parental  FYDLVRQINRKTPVEKKKPKK
          ..DL.RQINRKTP...K..KK
Retrocopy LHDLMRQINRKTPMAAKARKK

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_875 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 19 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Canis familiaris	ENSCAFG00000013686	1 retrocopy	retro_cfam_696,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Equus caballus	ENSECAG00000016434	1 retrocopy	retro_ecab_99,
Erinaceus europaeus	ENSEEUG00000010446	2 retrocopies	retro_eeur_306, retro_eeur_361,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Homo sapiens	ENSG00000116473	1 retrocopy	retro_hsap_1364,
Myotis lucifugus	ENSMLUG00000010571	3 retrocopies	retro_mluc_2311, retro_mluc_2312, retro_mluc_2313,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963, retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Ochotona princeps	ENSOPRG00000003999	3 retrocopies	retro_opri_321, retro_opri_460, retro_opri_875 ,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Tarsius syrichta	ENSTSYG00000004521	3 retrocopies	retro_tsyr_1546, retro_tsyr_1829, retro_tsyr_2140,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,