RetrogeneDB ID: retro_opri_449

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1231:187604..188022(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA5
• Ensembl ID: ENSOPRG00000008863
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 5 [Source:HGNC Symbol;Acc:9534]

Sequence

>retro_opri_449
GGGGTTTTCCTAGCTGTGGAAAAGAGAATTACCTCCCCACTCGTGGAGCCCAGCAGCACTGAGAAAATCATGGAGATCAA
TGCTAACATAGGTTGTGCCATGAGTAGTCTAATTGCTGATGCTGAGACTTTAATTGATAAAGCAAGAATGGAGATGCAGA
ACCATTGGTTTACCTACAGTGAGACCATGACAGTGGAGAGTGGGACCCAGGCTGTGTCAAATTTGGCTCTGCAGTTTGGA
CAAGATGCAGATCTAGGTGCCATGTCTTGTCCCTTTGGGGTAGCACTGCTGTTTGGAGAAGTTGATGAAAAAGGACCCCA
ACTATTTCACATGGACCCATGTGGAACCTTCCGTACAGTGTGAGGCTCGAGCAATCGGCTCTGCCTCAGAGCTCCTTGCA
GGAATTTTATCACAAGTC

Alignment

ORF - retro_opri_449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.85 %
• Parental protein coverage: 58.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQ
          GV.LAVEKRITSPL.EPSS.EKI.EI.A.IGCAMS.LIADA.TLIDKAR.E.QNHWFTY.ETMTVES.TQ
Retrocopy GVFLAVEKRITSPLVEPSSTEKIMEINANIGCAMSSLIADAETLIDKARMEMQNHWFTYSETMTVESGTQ

Parental  AVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTF-VQCDARAIGSASEGAQSSLQE
          AVSNLALQFG..DAD.GAMS.PFGVALLFG.VDEKGPQLFHMDP.GTF.VQC.ARAIGSASE.....L..
Retrocopy AVSNLALQFG-QDADLGAMSCPFGVALLFGEVDEKGPQLFHMDPCGTF>VQCEARAIGSASELLAGILSQ

Parental  V
          V
Retrocopy V

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_449 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013670	1 retrocopy	retro_cpor_1063,
Equus caballus	ENSECAG00000011835	1 retrocopy	retro_ecab_1106,
Echinops telfairi	ENSETEG00000012916	1 retrocopy	retro_etel_1053,
Mus musculus	ENSMUSG00000068749	1 retrocopy	retro_mmus_52,
Ochotona princeps	ENSOPRG00000008863	1 retrocopy	retro_opri_449 ,
Rattus norvegicus	ENSRNOG00000019868	2 retrocopies	retro_rnor_1230, retro_rnor_658,
Sus scrofa	ENSSSCG00000006830	2 retrocopies	retro_sscr_1156, retro_sscr_1194,