RetrogeneDB ID: retro_opri_652

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2199:231049..231457(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMMP2L
• Ensembl ID: ENSOPRG00000000996
• Aliases: None
• Description: IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae) [Source:HGNC Symbol;Acc:14598]

Sequence

>retro_opri_652
ATGGCCCAGTCTCAAGGATGGGTGAAAAGATACTGCACGGCCTTTTGCAAAGGCTTCTTCGTGGCAGTGCCCGTGGCAGT
GACTTTGCTGGACCGAGTTGCCTGCGTGGCGAGAGTGGAAGGCACATCAATGCAACCTTCTTTGAATCCTGGGGGGAGCC
GGTCACCTGATGTGGTACTTTTGAACCACTGGAAAGTGAGGAATTTTGAAGTTCAACGTGGTGACATTGTGTCGTTGGTG
TCTCCTAAAAACCCACAGCAGAAAATCATTAAGCGAGTGATTGCTCTTGAAGGAGATATTATCAGAACCATTGGACACAA
AAACCGGTATGTCAGAGTCCCCCGTGGTCACATCTGGGTCGAAGGTGATCACCATGGACACAGTTTTGACAGTAATTCCT
TTGGGCCC

Alignment

ORF - retro_opri_652 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQSQGWVKRYFKAFCKGFFVAVPVAVTVLDRVACVARVEGASMQPCLNPGGSQSSDVVLLNHWKVRNFE
          MAQSQGWVKRY..AFCKGFFVAVPVAVT.LDRVACVARVEG.SMQP.LNPGGS.S.DVVLLNHWKVRNFE
Retrocopy MAQSQGWVKRYCTAFCKGFFVAVPVAVTLLDRVACVARVEGTSMQPSLNPGGSRSPDVVLLNHWKVRNFE

Parental  VQRGDIVSLVSPKNPQQKIIKRVIALEGDIIRTIGHKNRYVKVPRGHIWVEGDHHGHSFDSNSFGP
          VQRGDIVSLVSPKNPQQKIIKRVIALEGDIIRTIGHKNRYV.VPRGHIWVEGDHHGHSFDSNSFGP
Retrocopy VQRGDIVSLVSPKNPQQKIIKRVIALEGDIIRTIGHKNRYVRVPRGHIWVEGDHHGHSFDSNSFGP

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_652 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000000996	2 retrocopies	retro_opri_652 , retro_opri_90,