RetrogeneDB ID: retro_opri_351

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_580:46895..47186(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf123
• Ensembl ID: ENSOPRG00000009003
• Aliases: None
• Description: chromosome 1 open reading frame 123 [Source:HGNC Symbol;Acc:26059]

Sequence

>retro_opri_351
AAAATTGTGTAGCAACTTAAAGCCACACTGGACAATGTCAGCAATCTGCGGCCTGTGGGCGAGGACTTCCACTGGCACCT
CAATATGAAATGTGGTGAGGTTTTGGAGAAGTGGCAGTACATCCACCAGATGGATAGTGTGGCCCTAAAGGGTGGCCAAG
GCAGCACCTCTGTGGCAGAACTGTGTGCGTGGGAAGACTCCATCAAAATTCTGAGCAGCACAATCAAGTCTTATAACGTT
GAAGACAATGACAAGTTCAAGACAACAGTCACGTTTGAATGTCGGGGCCTC

Alignment

ORF - retro_opri_351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.93 %
• Parental protein coverage: 65.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KIALQIRATLENVTNLRPVGEDFRWYLKMKCGNCGEISDKWQYIRQMDSVALKGGRGSASSVQKCKLCAR
          KI..Q..ATL.NV.NLRPVGEDF.W.L.MK...CGE...KWQYI.QMDSVALKGG.GS.S......LCA.
Retrocopy KIV*QLKATLDNVSNLRPVGEDFHWHLNMK---CGEVLEKWQYIHQMDSVALKGGQGSTSVAE---LCAW

Parental  ENSIGILSNTIKSYNAEDNEKFKTIVEFECRGL
          E.SI.ILS.TIKSYN.EDN.KFKT.V.FECRGL
Retrocopy EDSIKILSSTIKSYNVEDNDKFKTTVTFECRGL

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_351 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004526	3 retrocopies	retro_cjac_2948, retro_cjac_3149, retro_cjac_3186,
Cavia porcellus	ENSCPOG00000011509	1 retrocopy	retro_cpor_1142,
Homo sapiens	ENSG00000162384	1 retrocopy	retro_hsap_192,
Gorilla gorilla	ENSGGOG00000004027	1 retrocopy	retro_ggor_271,
Microcebus murinus	ENSMICG00000006397	1 retrocopy	retro_mmur_1113,
Myotis lucifugus	ENSMLUG00000002439	1 retrocopy	retro_mluc_101,
Mus musculus	ENSMUSG00000028608	1 retrocopy	retro_mmus_975,
Nomascus leucogenys	ENSNLEG00000017988	1 retrocopy	retro_nleu_1001,
Oryctolagus cuniculus	ENSOCUG00000029317	1 retrocopy	retro_ocun_770,
Otolemur garnettii	ENSOGAG00000013324	1 retrocopy	retro_ogar_861,
Ochotona princeps	ENSOPRG00000009003	2 retrocopies	retro_opri_351 , retro_opri_711,
Pongo abelii	ENSPPYG00000001336	1 retrocopy	retro_pabe_443,
Pan troglodytes	ENSPTRG00000000752	1 retrocopy	retro_ptro_99,
Rattus norvegicus	ENSRNOG00000012724	3 retrocopies	retro_rnor_1999, retro_rnor_2403, retro_rnor_2705,