RetrogeneDB ID: retro_opri_1202

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_9367:13743..13979(-)
• 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_1202
GAAGGGGATGCTAAAGGAGCTAACGCCAAGGTAAACAACAAACCACAGAGAGGATCGGCCAGCTTGTCTGCCAAACCAGC
TCCTGCAAAGCCAGAGCCCAAGCCTAAAAAGGGAGAGAAGGCATCAAAAGGGAAAAATGGAAAAGCCGATGCTGACAACA
ACGGGAATAACCCTACAGAACATGGAGATGCCCAACAGACCATGCACAGAAAGCCAAAGGTGCTGGAGATGCCAGG

Alignment

ORF - retro_opri_1202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.53 %
• Parental protein coverage: 98.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKDGNNPAENGDAK
          EGDAKG..AKV...PQR.SA.LSAKPAP.KPEPKPKK....K..K...GK...ADA...GNNP.E.GDA.
Retrocopy EGDAKGANAKVNNKPQRGSASLSAKPAPAKPEPKPKK--GEKASKGKNGK---ADADNNGNNPTEHGDAQ

Parental  -TDQAQKTEGAGDAK
          .TD.AQK..GAGDA.
Retrocopy <TDHAQKAKGAGDAR

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_1202 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,