RetrogeneDB ID: retro_opri_94

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2187:49643..49973(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD9
• Ensembl ID: ENSOPRG00000010271
• Aliases: None
• Description: COMM domain containing 9 [Source:HGNC Symbol;Acc:25014]

Sequence

>retro_opri_94
AATTTCCACCAAAACCTCAAAAACCTGCTGACAAAAATCATCCTAGAGCATGTATCCACATGAAGAACGGAAGCCCAAGC
AAATCAGATCTCTCTGCCGCGCCTGGTTGACCTGGACTGGAGAGTGGACATCAAAACCTCCTCGGATACCATCAGCCGCA
TGGCTGTCCCCACCTGCCTGCTCCAGATGAAGATCCAAGAAGATCCCAGTCTGTGTGGGGACAAACCCTCCGTCTCGGCC
GTCACCATGGAGCTGAGCAAGGAGACCCTGGACACCATGCTGGATGGGCTGGGCCGCATCCGTGACCAGCTTTCCGCTGT
GGCCAGCAAA

Alignment

ORF - retro_opri_94 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.27 %
• Parental protein coverage: 55.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NFHQNLK-LLTKILLEHVSTWRTEAQANQISLPRLVDLDWRVDIKTSSDTISRMAVPTCLLQMKIQEDPS
          NFHQNLK.LLTKI.LEHVST.RTEAQANQISLPRLVDLDWRVDIKTSSDTISRMAVPTCLLQMKIQEDPS
Retrocopy NFHQNLKNLLTKIILEHVST*RTEAQANQISLPRLVDLDWRVDIKTSSDTISRMAVPTCLLQMKIQEDPS

Parental  LCGDKPSVSAVTMELSKETLDTMLDGLGRIRDQLSAVASK
          LCGDKPSVSAVTMELSKETLDTMLDGLGRIRDQLSAVASK
Retrocopy LCGDKPSVSAVTMELSKETLDTMLDGLGRIRDQLSAVASK

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_94 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000027163	2 retrocopies	retro_mmus_3347, retro_mmus_731,
Ochotona princeps	ENSOPRG00000010271	2 retrocopies	retro_opri_848, retro_opri_94 ,