RetrogeneDB ID: retro_opri_148

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2858:943551..943869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB6
• Ensembl ID: ENSOPRG00000007428
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa [Source:HGNC Symbol;Acc:7701]

Sequence

>retro_opri_148
ATGTCGGGGTACACGCTGGATGAGAAACTGCGGCTGCAGCAGCTGCGAGAGCTGAGGCAACGATGGCTGAAGGACCAGGA
GCTGAGCGCTTGGGAGCCAGTGCAGCCCCCGCAGAGGACATGGCCCTTGGAGAGGTTCTGGAATAAGTTTCTGCAGAATG
AGGCCCCTTGGAGGAAGTTGGTCTATAAAACATACTGGCACAGCATCTTTGTTTTCACTCATGCACTTATACCTGCATAG
CTTATTCATTATTATTTCAAATATCATGTGAATACAAAACCGTATACCATGGTTCAGAGGAAGCCCAGAATATTCCCA

Alignment

ORF - retro_opri_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGYTPDEKLRLQQLRELRRRWLKDQELSAREPVQPPQRTWPLERFWNKFLQNEAPWRKMVYKTYRHSIF
          MSGYT.DEKLRLQQLRELR.RWLKDQELSA.EPVQPPQRTWPLERFWNKFLQNEAPWRK.VYKTY.HSIF
Retrocopy MSGYTLDEKLRLQQLRELRQRWLKDQELSAWEPVQPPQRTWPLERFWNKFLQNEAPWRKLVYKTYWHSIF

Parental  VFTHALIPAWLIHYYFKYHVVTKPYTMVQRKPRIFP
          VFTHALIPA.LIHYYFKYHV.TKPYTMVQRKPRIFP
Retrocopy VFTHALIPA*LIHYYFKYHVNTKPYTMVQRKPRIFP

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_148 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001263	3 retrocopies	retro_acar_110, retro_acar_116, retro_acar_117,
Callithrix jacchus	ENSCJAG00000007852	3 retrocopies	retro_cjac_1287, retro_cjac_255, retro_cjac_303,
Dasypus novemcinctus	ENSDNOG00000019864	2 retrocopies	retro_dnov_2281, retro_dnov_920,
Ochotona princeps	ENSOPRG00000007428	5 retrocopies	retro_opri_148 , retro_opri_525, retro_opri_591, retro_opri_614, retro_opri_722,
Sus scrofa	ENSSSCG00000011003	1 retrocopy	retro_sscr_260,
Tupaia belangeri	ENSTBEG00000013268	2 retrocopies	retro_tbel_195, retro_tbel_197,
Tarsius syrichta	ENSTSYG00000002785	1 retrocopy	retro_tsyr_382,
Tursiops truncatus	ENSTTRG00000012172	1 retrocopy	retro_ttru_1505,