RetrogeneDB ID: retro_opri_441

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1218:168410..169148(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX11
• Ensembl ID: ENSOPRG00000004138
• Aliases: None
• Description: cytochrome c oxidase assembly homolog 11 (yeast) [Source:HGNC Symbol;Acc:2261]

Sequence

>retro_opri_441
TGGGCTGCGGACGGGGCGGAAGCGTTCCTCAGACGGGCATGGAGCGGGACAGGAAGTGCTGAGACGGGGCTGAGGTGGCG
GCACGGGACATGGAAGCGCCCGAACCTGGCCGGGCAGCCCGGGCGGCGGCCGAAGAGCACGAACCCGTTCACGCGCGCCC
AGGAGGAGGACTGGCGGCGGCGGAACAAGACGGTGCTCACGTACGTGGCCGCGGCCGCCGTGGGCATGCTGGGGGCGTCT
TACGCCGCGGTGCCCCTCTATCGGCTCTATTGCCAGACTACCGGGCTTGGAGGATCAGCAGTAGCAGGTCATGGATCAGA
CCAAATTGAAAACATGGTACCCGTTAAGGATCGGATCATCAAAGTCACCTTTAATGCAGATGTGCACGCCAGTCTGCAGT
GGAACTTCAGACCTCAGCAGACGGAAATATATGTGGTGCCAGGAGAGACTGCATTAGCGTTTTATAAAGCAAAGAATCCT
ACTGACAAACCAGTGATTGGAATTTCTACGTACAATGTTGTACCATTTGAAGCTGGGCAATATTTCAATAAAATACAGTG
TTTCTGTTTTGAAGAACAAAGGCTTAATCCCCAAGAGGAGGTGGATATGCCAGTGTTTTTCTACATTGATCCTGAATTTG
CTGAAGGTCCAAGAATAGTGAATGTTGATCTTATCACTCTTTTCTATACTTTTTTTGAAGCAAAAGAAGGACACAAATTG
CCCATCCCAGGGTATAAC

Alignment

ORF - retro_opri_441 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.56 %
• Parental protein coverage: 90.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WAADGAEAFPRRAWSGTGSAETGLRWRHGTWKRPN-ARQPGRRPKSTNPFTRAQEEDWRRRNKTVLTYVA
          WAADGAEAF.RRAWSGTGSAETGLRWRHGTWKRPN.A.QPGRRPKSTNPFTRAQEEDWRRRNKTVLTYVA
Retrocopy WAADGAEAFLRRAWSGTGSAETGLRWRHGTWKRPNLAGQPGRRPKSTNPFTRAQEEDWRRRNKTVLTYVA

Parental  AAAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHGSDQIENMVPVKDRIIKVTFNADVHASLQWNFRPQQ
          AAAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHGSDQIENMVPVKDRIIKVTFNADVHASLQWNFRPQQ
Retrocopy AAAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHGSDQIENMVPVKDRIIKVTFNADVHASLQWNFRPQQ

Parental  TEIYVVPGETALAFYKAKNPTDKPVIGISTYNVVPFEAGQYFNKIQCFCFEEQRLNPQEEVDMPVFFYID
          TEIYVVPGETALAFYKAKNPTDKPVIGISTYNVVPFEAGQYFNKIQCFCFEEQRLNPQEEVDMPVFFYID
Retrocopy TEIYVVPGETALAFYKAKNPTDKPVIGISTYNVVPFEAGQYFNKIQCFCFEEQRLNPQEEVDMPVFFYID

Parental  PEFAEDPRMVNVDLITLSYTFFEAKEGHKLPIPGYN
          PEFAE.PR.VNVDLITL.YTFFEAKEGHKLPIPGYN
Retrocopy PEFAEGPRIVNVDLITLFYTFFEAKEGHKLPIPGYN

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_441 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008482	1 retrocopy	retro_cpor_1340,
Dasypus novemcinctus	ENSDNOG00000014862	1 retrocopy	retro_dnov_1933,
Dipodomys ordii	ENSDORG00000001207	1 retrocopy	retro_dord_180,
Homo sapiens	ENSG00000166260	1 retrocopy	retro_hsap_3442,
Microcebus murinus	ENSMICG00000005225	1 retrocopy	retro_mmur_1119,
Monodelphis domestica	ENSMODG00000014855	1 retrocopy	retro_mdom_952,
Mus musculus	ENSMUSG00000020544	4 retrocopies	retro_mmus_1318, retro_mmus_2318, retro_mmus_2714, retro_mmus_986,
Nomascus leucogenys	ENSNLEG00000007990	1 retrocopy	retro_nleu_2297,
Ochotona princeps	ENSOPRG00000004138	1 retrocopy	retro_opri_441 ,
Pongo abelii	ENSPPYG00000008259	2 retrocopies	retro_pabe_156, retro_pabe_2847,
Pan troglodytes	ENSPTRG00000009422	1 retrocopy	retro_ptro_2335,
Rattus norvegicus	ENSRNOG00000046318	1 retrocopy	retro_rnor_1515,