RetrogeneDB ID: retro_opri_75

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1887:34445..34758(-)
• Located in intron of: ENSOPRG00000010539

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP19
• Ensembl ID: ENSOPRG00000010549
• Aliases: None
• Description: signal recognition particle 19kDa [Source:HGNC Symbol;Acc:11300]

Sequence

>retro_opri_75
CAGGCTGTTGAAAACCCCACGGCCACCGAGATTCAGGATGTGTGCTCAGCAGTCGGGCTGAACGTGTTTCTTGAGAAAAA
TAAAATGTATTCTCGAGAGTGGAACCGTGACGTTCAGTACCGTGGCCGTGTCCGGGTGCAGCTCAAGCAGGAGGATGGCA
GCCTCTGCCTGGGGCAGTTCCCCTCACGAAGTCGGTAATGTTGTATGCAGCAGAGATGATACCCAAACTGAAAACAAGGA
TGCAGAAGGTGGGAGGTGTGACCCCAGTGTCCAACAAGGAGATGGAGGCAAAAAAGGCAGAGGAAAGAAGAAG

Alignment

ORF - retro_opri_75 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.39 %
• Parental protein coverage: 80.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLGQFPSR-KSVMLY
          .AVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLGQFPSR.KSVMLY
Retrocopy QAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLGQFPSR<KSVMLY

Parental  AAEMIPKLKTRTQKAGG-GDPSVQQGDGGKKGRGKKK
          AAEMIPKLKTR.QK.GG..DPSVQQGDGGKKGRGKKK
Retrocopy AAEMIPKLKTRMQKVGG<CDPSVQQGDGGKKGRGKKK

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_75 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 23 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031549	5 retrocopies	retro_cfam_1207, retro_cfam_1717, retro_cfam_1791, retro_cfam_2174, retro_cfam_848,
Choloepus hoffmanni	ENSCHOG00000013452	2 retrocopies	retro_chof_2525, retro_chof_636,
Callithrix jacchus	ENSCJAG00000016512	4 retrocopies	retro_cjac_1117, retro_cjac_3059, retro_cjac_3144, retro_cjac_886,
Equus caballus	ENSECAG00000008895	1 retrocopy	retro_ecab_503,
Erinaceus europaeus	ENSEEUG00000007298	2 retrocopies	retro_eeur_593, retro_eeur_646,
Echinops telfairi	ENSETEG00000017132	4 retrocopies	retro_etel_1016, retro_etel_119, retro_etel_1268, retro_etel_1599,
Felis catus	ENSFCAG00000025895	1 retrocopy	retro_fcat_1732,
Homo sapiens	ENSG00000153037	1 retrocopy	retro_hsap_835,
Macropus eugenii	ENSMEUG00000012529	2 retrocopies	retro_meug_1220, retro_meug_1596,
Microcebus murinus	ENSMICG00000000399	1 retrocopy	retro_mmur_502,
Myotis lucifugus	ENSMLUG00000014793	3 retrocopies	retro_mluc_1097, retro_mluc_350, retro_mluc_710,
Macaca mulatta	ENSMMUG00000000331	2 retrocopies	retro_mmul_1088, retro_mmul_1970,
Monodelphis domestica	ENSMODG00000013278	3 retrocopies	retro_mdom_1366, retro_mdom_1880, retro_mdom_663,
Mustela putorius furo	ENSMPUG00000012695	2 retrocopies	retro_mputfur_602, retro_mputfur_706,
Mus musculus	ENSMUSG00000014504	3 retrocopies	retro_mmus_1680, retro_mmus_3241, retro_mmus_686,
Nomascus leucogenys	ENSNLEG00000011571	1 retrocopy	retro_nleu_3068,
Oryctolagus cuniculus	ENSOCUG00000015639	3 retrocopies	retro_ocun_1003, retro_ocun_1548, retro_ocun_729,
Otolemur garnettii	ENSOGAG00000008579	1 retrocopy	retro_ogar_2070,
Ochotona princeps	ENSOPRG00000010549	3 retrocopies	retro_opri_400, retro_opri_75 , retro_opri_793,
Pongo abelii	ENSPPYG00000029584	1 retrocopy	retro_pabe_1569,
Pteropus vampyrus	ENSPVAG00000004895	1 retrocopy	retro_pvam_1465,
Rattus norvegicus	ENSRNOG00000020204	2 retrocopies	retro_rnor_1340, retro_rnor_997,
Ictidomys tridecemlineatus	ENSSTOG00000000348	2 retrocopies	retro_itri_318, retro_itri_831,