RetrogeneDB ID: retro_opri_1144

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_7914:43148..43737(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPX4
• Ensembl ID: ENSOPRG00000008347
• Aliases: None
• Description: glutathione peroxidase 4 [Source:HGNC Symbol;Acc:4556]

Sequence

>retro_opri_1144
ATGCTGCTGGGCCGCCTGAGCCGCTTGCTGAAGCCGGCATTGCTGTGTGGGGCCTTGGCCGCTCCAGGGCTGGCGGGCAC
CATGTGTGCATCCCGTGATGACTGGCGCTGCGCGCGCTCCATACATGAGTTCTCCACCAAGGACATCGACGGGCGCATGG
TGTGCCTGGACAAGTACCGGGGCTTCGTGTGCATCGTCACCAACGTAGCCTCCCAATGAGGCAAGGCAGAGGTGAACTAC
ACTCAGCTGGTCGACCTGCACGCGCGATACGCTGAGTGTGGTTTGCGCATCCTGGCCTTTCCCTGCAACCAGTTTGGGAG
GCAGGAGCCAGGGAGTAACGCGGAGATCAAAGAGTTCGCCGCCAGCTACAATGTCAAGTTTGATATGTACAGCAAGATCT
GCGTGAATGGCGACGATGCACACCCGCTGTGGAAGTGGATGAAAGTCCAGTCCAAGGGCAGGGGCATGCTGGGCAACGCC
ATCAAGTGGAATTTCACCAAGTTCCTGGTGCACAAAAATGGTTGCGTGGTGAAGCGGTACGGTCCCATGAAGAGCCCCTG
TGATCGAGAAGGACCTGCCCTGCTATCTC

Alignment

ORF - retro_opri_1144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLLGRLSRLLKPALLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGRMVCLDKYRGFVCIVTNVA
          MLLGRLSRLLKPALLCGALAAPGLAGTMCASRDDWRCARS.HEFS.KDIDGRMVCLDKYRGFVCIVTNVA
Retrocopy MLLGRLSRLLKPALLCGALAAPGLAGTMCASRDDWRCARSIHEFSTKDIDGRMVCLDKYRGFVCIVTNVA

Parental  SQUGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGRQEPGSNAEIKEFAASYNVKFDMYSKICVNGDDA
          SQ.GK.EVNYTQLVDLHARYAECGLRILAFPCNQFGRQEPGSNAEIKEFAASYNVKFDMYSKICVNGDDA
Retrocopy SQ*GKAEVNYTQLVDLHARYAECGLRILAFPCNQFGRQEPGSNAEIKEFAASYNVKFDMYSKICVNGDDA

Parental  HPLWKWMKVQPKGRGMLGNAIKWNFTKFLVDKNGCVVKRYGPM-EEPL-VIEKDLPCYL
          HPLWKWMKVQ.KGRGMLGNAIKWNFTKFLV.KNGCVVKRYGPM.EEPL.VIEKDLPCYL
Retrocopy HPLWKWMKVQSKGRGMLGNAIKWNFTKFLVHKNGCVVKRYGPM<EEPL<VIEKDLPCYL

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_1144 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022744	1 retrocopy	retro_fcat_1113,
Monodelphis domestica	ENSMODG00000005486	1 retrocopy	retro_mdom_1363,
Mus musculus	ENSMUSG00000075706	2 retrocopies	retro_mmus_1595, retro_mmus_560,
Ochotona princeps	ENSOPRG00000008347	4 retrocopies	retro_opri_1144 , retro_opri_63, retro_opri_705, retro_opri_929,