RetrogeneDB ID: retro_opri_19

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1030:779202..780140(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMU1
• Ensembl ID: ENSOPRG00000011389
• Aliases: None
• Description: smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans) [Source:HGNC Symbol;Acc:18247]

Sequence

>retro_opri_19
ACATAGCTGAGCAGGCACATTAAGCTGGGTCAGAAATCCCATGTGGAGTGTGCTCAGTTTTCTCCAGATGGTCAGTGTCT
GGTCACTGGGCCTATAGATGGCTTCATTGAAGTGTAGAACTTCACCAGTGGAAAAATCCGGAAGGATCTTAAGTACCAGG
CCCAGGATAACTTTATGATGATGATGGACCAAGCTGTCCTGTGCCTGTGTTTCAGCAGAGACACAGAGATGTTAGCAACT
GGGGCTCAGGGTGGGAAGATCAAGGTGTGGAAGAGGCAGAGTGGACAGTGTTTAAGGAGGTTTGAGAGGGCAACGCAGCA
AAGGCATCACCCGTCTGAGCTTTTCTAAGGATAGCAGTCAGCTGCTTAGTGCCTCCTTTGACCAGACCATCAGATTCCAT
GGCTTAAGATCTGGGAAAACACTGAAGGGTTTCCGTGGCCATTCCTCCTTCGTTAATGAGGCAATATTTACAGAAGACGA
GCATTCCATCCTTAGCACGTCCTCTGACGGCACCGTAAAGATCTGGAATATGAAGACCACAGAATGTTCGAGTTCCTTTC
AACTCATGGGCGGTACCGCGGGGACAGACATTGCTGTGTACAGTGTGATCCTGTTTCCTAAGAACCCGCAGCATTTCGTG
GTGTGCAACAAGTCAAACACCGTGCTCATCATGAACGTGCAGGGGCAGATTGTCAGAAGCTTCAGCTCTGGTAAAAGAGA
AGGCGGTGACTTTGTCTGCTGTGCCCTCCTCCCGCAAGGCAGAAGGATCTACTGTGTTGGGGAGGACTTGGTGCTCTATT
GTTTCAGCACGCTCACTTGGCAAACTGCAGAGAACTTTGGCAGTTCATGAGAAGGATGTGATTGGCATTGCACATCACCC
TCATCAGAACCTGATCGCTACCTACAGTGAAGATGGACTCCTAAAGCTCTGGAAACCT

Alignment

ORF - retro_opri_19 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.39 %
• Parental protein coverage: 61.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TQLSRHIKFGQKSHVECARFSPDGQYLVTGSVDGFIEVWNFTTGKIRKDLKYQAQDNFMMM-DDAVLCMC
          T.LSRHIK.GQKSHVECA.FSPDGQ.LVTG..DGFIEV.NFT.GKIRKDLKYQAQDNFMMM.D.AVLC.C
Retrocopy T*LSRHIKLGQKSHVECAQFSPDGQCLVTGPIDGFIEV*NFTSGKIRKDLKYQAQDNFMMMMDQAVLCLC

Parental  FSRDTEMLATGAQDGKIKVWKIQSGQCLRRFERA-HSKGVTCLSFSKDSSQILSASFDQTIRIHGLKSGK
          FSRDTEMLATGAQ.GKIKVWK.QSGQCLRRFERA..SKG.T.LSFSKDSSQ.LSASFDQTIR.HGL.SGK
Retrocopy FSRDTEMLATGAQGGKIKVWKRQSGQCLRRFERA>RSKGITRLSFSKDSSQLLSASFDQTIRFHGLRSGK

Parental  TLKEFRGHSSFVNEATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKSLGSTAGTDITVNSVILLPKNP
          TLK.FRGHSSFVNEA.FT.D.H.I.S.SSDGTVKIWNMKTTECS..F...G.TAGTDI.V.SVIL.PKNP
Retrocopy TLKGFRGHSSFVNEAIFTEDEHSILSTSSDGTVKIWNMKTTECSSSFQLMGGTAGTDIAVYSVILFPKNP

Parental  EHFVVCNRSNTVVIMNMQGQIVRSFSSGKREGGDFVCCALSPRGEWIYCVGEDFVLYCFSTVT-GKLERT
          .HFVVCN.SNTV.IMN.QGQIVRSFSSGKREGGDFVCCAL.P.G..IYCVGED.VLYCFST.T.GKL.RT
Retrocopy QHFVVCNKSNTVLIMNVQGQIVRSFSSGKREGGDFVCCALLPQGRRIYCVGEDLVLYCFSTLT>GKLQRT

Parental  LTVHEKDVIGIAHHPHQNLIATYSEDGLLKLWKP
          L.VHEKDVIGIAHHPHQNLIATYSEDGLLKLWKP
Retrocopy LAVHEKDVIGIAHHPHQNLIATYSEDGLLKLWKP

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_19 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006212	1 retrocopy	retro_cpor_819,
Homo sapiens	ENSG00000122692	1 retrocopy	retro_hsap_457,
Gorilla gorilla	ENSGGOG00000014802	1 retrocopy	retro_ggor_440,
Myotis lucifugus	ENSMLUG00000016097	1 retrocopy	retro_mluc_213,
Monodelphis domestica	ENSMODG00000003439	1 retrocopy	retro_mdom_965,
Ochotona princeps	ENSOPRG00000011389	2 retrocopies	retro_opri_19 , retro_opri_741,
Pongo abelii	ENSPPYG00000019140	1 retrocopy	retro_pabe_274,
Pan troglodytes	ENSPTRG00000020853	1 retrocopy	retro_ptro_344,