RetrogeneDB ID: retro_opri_17

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4292:30280..30799(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000005937
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CETN3
• Ensembl ID: ENSOPRG00000002381
• Aliases: None
• Description: centrin, EF-hand protein, 3 [Source:HGNC Symbol;Acc:1868]

Sequence

>retro_opri_17
ATGGCGGCCAGCTTCAAGAAGCCAAACCCGGCCTCCACCAGCCAGAGGAAAAAGTCGTGTCCGAAGCCCGAACTCACTGA
AGAGCAGAAGCAGGAAGTTCGGGAGGCGTTTGACCTCTTCGATGCTGACGGAAGCGGCACCATCGACGTGAAGGAGCTGA
AGGTGGCCATGAGGGCGTTGGGCTTCGAACCCAAGAAGGAAGAGATCAAGAAAATGATCTCAGAGGTAGACAAGGAGGGC
ACGGGAAAGATCAGCTTCAATGACTTCCTGGCCGTGATGACTCAGAAGATGGCTGAGAAGGACACCAAAGAAGAAATCCT
GAAGGCATTCCGGCTCTTTGATGACGACGAGACAGGGAAGATATCTTTCAAAAATCTCAAGCGTGTGGCCAACGAGCTGG
GGGAGAACCTCACGGATGAGGAGCTGCAGGAAATGATCGACGAAGCAGATCGGGATGGAGACGGCGAAGTGAATGAAGAG
GAGTTCCTTAAGATCATGAAGAAGACCAGCCTCTATTAG

Alignment

ORF - retro_opri_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.28 %
• Parental protein coverage: 93.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTKRKKRRELSEEQRQEIKDAFELFDTDKDDAIDYHELKVAMRALGFDVKKADVLKILKDYDREATGKIT
          ..K.....EL.EEQ.QE...AF.LFD.D....ID..ELKVAMRALGF..KK....K.....D.E.TGKI.
Retrocopy RKKSCPKPELTEEQKQEVREAFDLFDADGSGTIDVKELKVAMRALGFEPKKEEIKKMISEVDKEGTGKIS

Parental  FEDFNEVVTDWILERDPHEEILKAFKLFDDDDSGKISLRNLRRVARELGENMSDEELRAMIEEFDKDGDG
          F.DF..V.T....E.D..EEILKAF.LFDDD..GKIS..NL.RVA.ELGEN..DEEL..MI.E.D.DGDG
Retrocopy FNDFLAVMTQKMAEKDTKEEILKAFRLFDDDETGKISFKNLKRVANELGENLTDEELQEMIDEADRDGDG

Parental  EINQEEFIAIM
          E.N.EEF..IM
Retrocopy EVNEEEFLKIM

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_17 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007233	1 retrocopy	retro_dord_30,
Otolemur garnettii	ENSOGAG00000002383	1 retrocopy	retro_ogar_3511,
Ochotona princeps	ENSOPRG00000002381	1 retrocopy	retro_opri_17 ,
Procavia capensis	ENSPCAG00000006854	1 retrocopy	retro_pcap_403,
Pteropus vampyrus	ENSPVAG00000017925	1 retrocopy	retro_pvam_19,
Tupaia belangeri	ENSTBEG00000001992	2 retrocopies	retro_tbel_4470, retro_tbel_4732,