RetrogeneDB ID: retro_opri_709

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_25122:43624..44016(-)
• 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_709
ATGGCAGCGCAGCAGCAGGACCGCGGGGCCCCCTCGCAGCAGGCAGGTCCCTGGCGGAGACCGACCCCTTGAGCTGCTTC
ACCTGTCCCGTGTGCTTAGAGGTTTATCACAAGCCGATTCAGGTGCCCTGCGGACATGTCCTTTGCTCTGCATACCTGCA
GGAGTGCCTGAAGCCCGTCTGTGGGGTGTGTCTCAACGCTCTGGCCCCTGGCGTCCCAGCTGTGGAGCTTGAACGACAGA
TCTAGAACACAGAGACTTCCTGCCATGGCTGCCATAAGAATTTCTTCCTTGCAAAGATCCGGGCCCACGTGGCTACCTGT
TCCAAATACCAGAGTTACATCATGGAAGGCGTGAAGGCCACCACCAAGGACACGTTCCTGCAGCAAAGGAAT

Alignment

ORF - retro_opri_709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 58.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAQQQDRGAPSQPAGP-AAETDPLSRFTCPVCLEVYDKPMQVPCGHVFCSACLQECLKPKKPVCGVCRN
          MAAQQQDRGAPSQ.AGP..AETDPLS.FTCPVCLEVY.KP.QVPCGHV.CSA.LQECL...KPVCGVC.N
Retrocopy MAAQQQDRGAPSQQAGP<LAETDPLSCFTCPVCLEVYHKPIQVPCGHVLCSAYLQECL---KPVCGVCLN

Parental  ALAPGVPAAELERQIERTETSCHGCRKNFFLSKIRAHVATCSKYQSYIMEGVKATTKDTSLQQRN
          ALAPGVPA.ELERQI..TETSCHGC.KNFFL.KIRAHVATCSKYQSYIMEGVKATTKDT.LQQRN
Retrocopy ALAPGVPAVELERQI*NTETSCHGCHKNFFLAKIRAHVATCSKYQSYIMEGVKATTKDTFLQQRN

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_709 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,