RetrogeneDB ID: retro_opri_368

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_10093:12253..12648(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF114
• Ensembl ID: ENSOPRG00000004732
• Aliases: None
• Description: ring finger protein 114 [Source:HGNC Symbol;Acc:13094]

Sequence

>retro_opri_368
ATGGCAGCGCAGCAGCAGGGACCGCGGGGCCCCCTCGCAGCAGGCAGGTCCCTGGCGGAGACGGACCCCTTGAGCTGCTT
CACCTGTCCCGTGTGCTTAGAGGTTTATCACAAGCCGATTTCAGGTGCCCTGCGACATGTCCTTTGCTCTGCATACCTGC
AGGAGTGCCTGAAGCCCGTCTGTGGGGTGTGTCTCAACGCTCTGGACCCTGGCGTCCCAGCTGGTGGAGCTTGAACGACA
GATCTAGAACACAGAGACTTCCTGCCATGGGCTGCCATAAGACTTTCTTCCTTGCAAAGATCCGGGCCCACGTGGCTACC
TGTTCCAAATACCAGAGTTACATCATGGAAGGCGTGAAGGCCACCACCAAGGACACGTTCCTGCAGCAAAGGAAT

Alignment

ORF - retro_opri_368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.43 %
• Parental protein coverage: 58.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAAQQQ-DRGAPSQPAGP-AAETDPLSRFTCPVCLEVYDKPM-QVPCG-HVFCSACLQECLKPKKPVCGV
          MAAQQQ.DRGAPSQ.AGP..AETDPLS.FTCPVCLEVY.KP..QVPC..HV.CSA.LQECL...KPVCGV
Retrocopy MAAQQQ>DRGAPSQQAGP<LAETDPLSCFTCPVCLEVYHKPI>QVPCD<HVLCSAYLQECL---KPVCGV

Parental  CRNALAPGVPAA-ELERQIERTETSCHG-CRKNFFLSKIRAHVATCSKYQSYIMEGVKATTKDTSLQQRN
          C.NAL.PGVPA..ELERQI..TETSCHG.C.K.FFL.KIRAHVATCSKYQSYIMEGVKATTKDT.LQQRN
Retrocopy CLNALDPGVPAG>ELERQI*NTETSCHG>CHKTFFLAKIRAHVATCSKYQSYIMEGVKATTKDTFLQQRN

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_368 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009113	2 retrocopies	retro_dnov_1534, retro_dnov_1557,
Microcebus murinus	ENSMICG00000011155	1 retrocopy	retro_mmur_992,
Otolemur garnettii	ENSOGAG00000003953	3 retrocopies	retro_ogar_1149, retro_ogar_2158, retro_ogar_2330,
Ochotona princeps	ENSOPRG00000004732	2 retrocopies	retro_opri_368 , retro_opri_709,
Ochotona princeps	ENSOPRG00000011494	1 retrocopy	retro_opri_554,
Pteropus vampyrus	ENSPVAG00000004117	4 retrocopies	retro_pvam_1136, retro_pvam_1148, retro_pvam_1149, retro_pvam_1477,
Sarcophilus harrisii	ENSSHAG00000001827	1 retrocopy	retro_shar_193,