RetrogeneDB ID: retro_opri_143

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2800:102507..102818(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB2
• Ensembl ID: ENSOPRG00000013184
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDa [Source:HGNC Symbol;Acc:7697]

Sequence

>retro_opri_143
ATGTCGGCTCTGTGCAGGCTAGCGCCTGTCATTCGCGCTGGAGGGTCTCTCTTAAGAGGTGGCCGCGTGCGGGCGGCTGG
AGGCAGCGGCGTCCGTCACGCTGGCGGCCACGTACACATCGAGCCACGGTACAGTTTCCCCAACTGACCAAAGGCCAGGT
GATCAGGGCGGAGCTGTTCAGCGCAACCATGTGGTTCTGGATTCTCTGGCGTTTTTGGCATGACTCCGATGCTGTGTGGG
GTCACTTTCCATATCCAGACCCTTCCCAGTGGACAGATGAAGAATTAGGGATCCTTCCTGATGATGAAGAC

Alignment

ORF - retro_opri_143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAVCRLVPVIRAGGSLLRGGRVRAAGGSGVRYAGGDVHIEPRYRQFP-QLTKGQVIRAELFSATMWFWI
          MSA.CRL.PVIRAGGSLLRGGRVRAAGGSGVR.AGG.VHIEPRY..FP.QLTKGQVIRAELFSATMWFWI
Retrocopy MSALCRLAPVIRAGGSLLRGGRVRAAGGSGVRHAGGHVHIEPRY-SFP<QLTKGQVIRAELFSATMWFWI

Parental  LWRFWHDSDAVLGHFPYPDPSQWTDEELGILPDDED
          LWRFWHDSDAV.GHFPYPDPSQWTDEELGILPDDED
Retrocopy LWRFWHDSDAVWGHFPYPDPSQWTDEELGILPDDED

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_143 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011176	1 retrocopy	retro_acar_138,
Canis familiaris	ENSCAFG00000003930	3 retrocopies	retro_cfam_1673, retro_cfam_2184, retro_cfam_958,
Equus caballus	ENSECAG00000000877	1 retrocopy	retro_ecab_587,
Mustela putorius furo	ENSMPUG00000003423	3 retrocopies	retro_mputfur_132, retro_mputfur_1443, retro_mputfur_207,
Mus musculus	ENSMUSG00000002416	1 retrocopy	retro_mmus_1881,
Otolemur garnettii	ENSOGAG00000009644	1 retrocopy	retro_ogar_1405,
Ochotona princeps	ENSOPRG00000013184	2 retrocopies	retro_opri_1201, retro_opri_143 ,
Rattus norvegicus	ENSRNOG00000026616	2 retrocopies	retro_rnor_1153, retro_rnor_2449,
Sarcophilus harrisii	ENSSHAG00000015924	1 retrocopy	retro_shar_639,
Sus scrofa	ENSSSCG00000016495	1 retrocopy	retro_sscr_1149,
Ictidomys tridecemlineatus	ENSSTOG00000002566	1 retrocopy	retro_itri_1100,
Tursiops truncatus	ENSTTRG00000000547	2 retrocopies	retro_ttru_1567, retro_ttru_1910,