RetrogeneDB ID: retro_opri_721

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2588:87819..88266(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000011443
• Aliases: None
• Description: None

Sequence

>retro_opri_721
ATGGCGGCTCAAATTCCCATCGTGGCCACCACTTCCACTCCCGGGATAGCCCGCAGCAGTAAGAAGAGGCCTGCCAGCCC
TTCCCACAACGGCAGCAGCGGCAGAGCCTACAGTGCCAGTAAGAAGAAAAAAGTGTCTGGCTCTAGCTTCGCGCAGGGTA
TCGGCATGGATGCCATGAGTGAGAGTAAAATGGTGCCCTCTGACTTTAACGCCGGACCTATGGAAAAAGCTGCCAAACCT
TTGCCGTTTAAGGATCTCAACTTTGTGCACTCTGGCCATGGTGGTGCAGTAGCTGGCAAGAAAAACAGAACCTGGAAGCA
CCTGAAACAAATTCTGGCTGCTGAAAGGGCCTTACTGTGGCCGCTGAACGACCCTAACTACTTCAGTATTGATGCTCCTC
CATCCTTTAAGCCAGCTAAGAAGTATTCTGATGTTTCAGGCCTTCTT

Alignment

ORF - retro_opri_721 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAQIPIVATTSTPGIARSSKKRPASPSHNGSSGGAYSASKKKKVSGSSFAQGIGMDAMTESKMVPSDFN
          MAAQIPIVATTSTPGIARSSKKRPASPSHNGSSG.AYSASKKKKVSGSSFAQGIGMDAM.ESKMVPSDFN
Retrocopy MAAQIPIVATTSTPGIARSSKKRPASPSHNGSSGRAYSASKKKKVSGSSFAQGIGMDAMSESKMVPSDFN

Parental  AGPMEKAAKPLPFKDPNFVHSGHGGAVAGKKNRTWKNLKQILAAERALPWQLNDPNYFSIDAPPSFKPAK
          AGPMEKAAKPLPFKD.NFVHSGHGGAVAGKKNRTWK.LKQILAAERAL.W.LNDPNYFSIDAPPSFKPAK
Retrocopy AGPMEKAAKPLPFKDLNFVHSGHGGAVAGKKNRTWKHLKQILAAERALLWPLNDPNYFSIDAPPSFKPAK

Parental  KYSDVSGLL
          KYSDVSGLL
Retrocopy KYSDVSGLL

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_721 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
Canis familiaris	ENSCAFG00000017884	1 retrocopy	retro_cfam_371,
Myotis lucifugus	ENSMLUG00000030708	3 retrocopies	retro_mluc_118, retro_mluc_1892, retro_mluc_1942,
Macaca mulatta	ENSMMUG00000020108	1 retrocopy	retro_mmul_1340,
Ochotona princeps	ENSOPRG00000011443	1 retrocopy	retro_opri_721 ,
Pteropus vampyrus	ENSPVAG00000017436	1 retrocopy	retro_pvam_899,