RetrogeneDB ID: retro_opri_161

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3036:515629..515809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000001616
• Aliases: None
• Description: None

Sequence

>retro_opri_161
AGCAGAGTCAAGGACAACCACGAAGATGTTCTGCAAGCTTTCCTGTCAGTCTGCTCCTCCAACCCTACAGTCAACGCCTA
AATGGCCCATGCTAAAAAGGGAGAGGAAGTTCCCAAAGAGAAAAAAGGAAGAATTGATGCGAGCAAAAATCGAACTAATC
CTGCAGCAGAAAATGAGGAC

Alignment

ORF - retro_opri_161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.69 %
• Parental protein coverage: 70.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AKVKD-EPQRRSA-RLSAKPAPPKPEPKPK-KAPAKKGEKVPKGKKGKADAGKDGNNP-AENGD
          ..VKD..P.R.SA..LS...APP.....PK..A.AKKGE.VPK.KKG..DA.K...NP.AEN.D
Retrocopy SRVKD<QPRRCSA<KLSCQSAPPTLQSTPK<MAHAKKGEEVPKEKKGRIDASKNRTNPAAENED

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_161 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 4 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000012812	3 retrocopies	retro_fcat_1842, retro_fcat_4, retro_fcat_530,
Mus musculus	ENSMUSG00000003038	2 retrocopies	retro_mmus_202, retro_mmus_2582,
Ochotona princeps	ENSOPRG00000001616	5 retrocopies	retro_opri_1202, retro_opri_161 , retro_opri_532, retro_opri_730, retro_opri_853,
Tursiops truncatus	ENSTTRG00000005681	5 retrocopies	retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,