RetrogeneDB ID: retro_opri_1135

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_7788:7533..7790(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP9
• Ensembl ID: ENSOPRG00000012133
• Aliases: None
• Description: signal recognition particle 9kDa [Source:HGNC Symbol;Acc:11304]

Sequence

>retro_opri_1135
ATACCTAAGCAGCAGACATGGGAAGAGGTCACCGCGTGACCCAGAGGCTCTACCTCGCTGACCCCATGAAGGCACGTGCG
GTTTTCAAAGATAGACTTTCTGACGGAAGTTTGTGCATTAAAGTAACAGATGATTTAGTTTGTTTGGTGTATAGAACAGA
CTAAGCTCAAGATGTAAAGGAGGTTGAGACATTCTACAGTCAGCTAATGTGACTTATGGTAGCTAAGGAATCCCACAGTG
TTGCCATGGAAACAAAC

Alignment

ORF - retro_opri_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPQYQTWEEFS-RAAEKLYLADPMKARVVLKYRHSDGSLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQL
          .P..QTWEE...R....LYLADPMKAR.V.K.R.SDGSLCIKVTDDLVCLVYRTD.AQDVK..E.F.SQL
Retrocopy IPKQQTWEEVT<RVTQRLYLADPMKARAVFKDRLSDGSLCIKVTDDLVCLVYRTD*AQDVKEVETFYSQL

Parental  MRLMVAKESRSVAMETD
          M.LMVAKES.SVAMET.
Retrocopy M*LMVAKESHSVAMETN

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_1135 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014744	2 retrocopies	retro_amel_1168, retro_amel_898,
Echinops telfairi	ENSETEG00000012291	1 retrocopy	retro_etel_272,
Homo sapiens	ENSG00000143742	1 retrocopy	retro_hsap_711,
Otolemur garnettii	ENSOGAG00000001752	1 retrocopy	retro_ogar_230,
Ochotona princeps	ENSOPRG00000012133	2 retrocopies	retro_opri_1135 , retro_opri_324,