RetrogeneDB ID: retro_opri_477

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_13319:44965..45722(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBAP1
• Ensembl ID: ENSOPRG00000009100
• Aliases: None
• Description: ubiquitin associated protein 1 [Source:HGNC Symbol;Acc:12461]

Sequence

>retro_opri_477
TCTGGGTCCGTGTTACAGGATGAGGTCCTGGCAACACTGTAGCTGGAAACCTTGGCTTCAAGCCTCTTTGCAAACCCAAT
GGCTTTGTAACCTTACCACAGTTGGGCAACTGTGAAAAGATGTTGTTGTCTTCCAAAGTGTCCCTTACCCCAATTCCTGC
AGTAAGCAGTATCAAATCCCTATCCTTTCCCAAACTTGACTCTGATGACAGCAATCAGCAGACAGCCAAACTGGCAAGCA
CTTTCCATAGCACATCCTGCCTCCGCAGTGGCACACTCTTGAACTCCCTCAAGCCTTTCACCCAAAGCAATGCCAGCGAG
CTCAATAGACATCATACTGTTGGGCTTTCAGATTTGGACTAAGACAGGGGCACTGAGGTGCTCACCCTTGCTTCCTCCCA
GATGCCTTCCCGCTCAGTCTCGTCTGTGTGCACAGAACAGTCATCACCTTTACAGGCAGGCTCCACAGTCACCCCTCCTA
ATTTCTCAATATCACAAGTGCTTAGCTGCCCCCAGGCCTGCTCTGAGCTGCAGGCATTGTCCCCCAGCAAGTAGCAGTGT
GTGGAGACAATGGCCAACATGGGCTACTCCTATGAGTGTGTCGTAAGAGCCAGGAAGAAGAAAGGAGAGACTATTGAGCA
GATTTTCGACTATCTCTTTGTATGTGGACAACTTTCTGAGAAGGGCTTTGACCCTCTATGGTGGGAGCAGCTTTGGAAAT
GCACCAGCGTTCAGAAGAAAAAATAATGGAGCTTCTA

Alignment

ORF - retro_opri_477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.91 %
• Parental protein coverage: 50.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGSVLQDEEVLASLERATL-DFKPLHKPNGFITLPQLGNCEKMSLSSKVSLPPIPAVSNIKSLSFPKLDS
          SGSVLQDE.VLA.L...TL..FKPL.KPNGF.TLPQLGNCEKM.LSSKVSL.PIPAVS.IKSLSFPKLDS
Retrocopy SGSVLQDE-VLATL*LETL<GFKPLCKPNGFVTLPQLGNCEKMLLSSKVSLTPIPAVSSIKSLSFPKLDS

Parental  DDSNQKTAKLASTFHSTSCLRSGTLLNSFKPSTQSSASELNGHHTLGLSALNLDSGTEVPTLAPSQTPSH
          DDSNQ.TAKLASTFHSTSCLRSGTLLNS.KP.TQS.ASELN.HHT.GLS.L..D.GTEV.TLA.SQ.PS.
Retrocopy DDSNQQTAKLASTFHSTSCLRSGTLLNSLKPFTQSNASELNRHHTVGLSDLD*DRGTEVLTLASSQMPSR

Parental  SVLSVCTEESSPPQAGSAVAPPNFSMSQVPSCPQAYSELQTLSPSERQCVETVVNMGYSYDCVLRAMKKK
          SV.SVCTE.SSP.QAGS.V.PPNFS.SQV.SCPQA.SELQ.LSPS..QCVET..NMGYSY.CV.RA.KKK
Retrocopy SVSSVCTEQSSPLQAGSTVTPPNFSISQVLSCPQACSELQALSPSK*QCVETMANMGYSYECVVRARKKK

Parental  GENIEQILDYLFAHGQLCEKGFDPL-LVEEALEMHQCSEEKMMEFL
          GE.IEQI.DYLF..GQL.EKGFDPL..V..ALEMHQ.SEEK.ME.L
Retrocopy GETIEQIFDYLFVCGQLSEKGFDPL<MVGAALEMHQRSEEKIMELL

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_477 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000011672	1 retrocopy	retro_eeur_466,
Myotis lucifugus	ENSMLUG00000013063	1 retrocopy	retro_mluc_2305,
Otolemur garnettii	ENSOGAG00000015802	1 retrocopy	retro_ogar_557,
Ochotona princeps	ENSOPRG00000009100	3 retrocopies	retro_opri_355, retro_opri_477 , retro_opri_680,
Ictidomys tridecemlineatus	ENSSTOG00000028294	1 retrocopy	retro_itri_1318,
Tarsius syrichta	ENSTSYG00000013035	2 retrocopies	retro_tsyr_1908, retro_tsyr_846,