RetrogeneDB ID: retro_opri_964

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_50799:5149..5671(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000013867
• Aliases: None
• Description: None

Sequence

>retro_opri_964
CTTTACAATATCATCATGTCTTATGAAGTCTGTGCCTGGCTCATAGTTGGAGTGTACATCGTGAGTTTGGTTGGTGCCAT
GGTACATACTATTTGTATGCTAAGGGTTTTTTTCTGTAAGGCTGATATAATCAATCATTACTTCTGTGATCTTTTTCCAC
TACTGAGACTTTCCTGTTCCAGTACTTATGTCAATGAGGTTGTACTTTTGTGCTTCAGCACATTCAACATCCTTGTTCCA
GTGCTGATCATCCTCAGCTCTTACAGCTTCATCATTCACAGCATCCTGGGCATCCATTCCACCAAGGGTCGGTCCAAGGC
CTTCAGCACCTGCAGCTCTCATTTTTTAGCTGTTGGCTTGTTTTTTGGTTCTCTGGCGTTTATGTACCTACAGCCATCAT
CTGGCAATGACCTTGGCCAAAACAAAGTGTCTTCTGTAATTTATACCATTATTGTACCCATGTTGAATCCACTTATCTAC
AGTTTGAGGAATAAAGATGTTAAGGTTGCCCTTAACAAGGTA

Alignment

ORF - retro_opri_964 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.53 %
• Parental protein coverage: 57.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYNIIMSYEVCAWLIVGVYIVSLVGAMVHTICMLRVFFCKADIINHYFCDLFPLLRLSCSSTYVNEVVLL
          LYNIIMSYEVCAWLIVGVYIVSLVGAMVHTICMLRVFFCKADIINHYFCDLFPLLRLSCSSTYVNEVVLL
Retrocopy LYNIIMSYEVCAWLIVGVYIVSLVGAMVHTICMLRVFFCKADIINHYFCDLFPLLRLSCSSTYVNEVVLL

Parental  CFSTFNILVPVLIILSSYSFIIHSILGIHSTKGRSKAFSTCSSHFLAVGLFFGSLAFMY-SPSSLNSMDQ
          CFSTFNILVPVLIILSSYSFIIHSILGIHSTKGRSKAFSTCSSHFLAVGLFFGSLAFMY..PSS.N...Q
Retrocopy CFSTFNILVPVLIILSSYSFIIHSILGIHSTKGRSKAFSTCSSHFLAVGLFFGSLAFMYLQPSSGNDLGQ

Parental  GKVSSVFYTIIVPMLNPLIYSLRNKDVHIAMKKI
          .KVSSV.YTIIVPMLNPLIYSLRNKDV..A..K.
Retrocopy NKVSSVIYTIIVPMLNPLIYSLRNKDVKVALNKV

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_964 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013370	4 retrocopies	retro_meug_2060, retro_meug_2076, retro_meug_35, retro_meug_447,
Ochotona princeps	ENSOPRG00000013867	1 retrocopy	retro_opri_964 ,