RetrogeneDB ID: retro_opri_287

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4660:134862..135172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX20
• Ensembl ID: ENSOPRG00000004534
• Aliases: None
• Description: COX20 cytochrome C oxidase assembly factor [Source:HGNC Symbol;Acc:26970]

Sequence

>retro_opri_287
AAGACTTTTCAACTTCTAGGAATTTTAGGTATCAAAAACACTTCTGTGCACGGGCTTCAGTACTGAATGGGTCCCTGGGA
TCTGCTGCGCTGGCCTTGAACTTCTGTGTTAACTAAATCTTCTTAGAAGATCATGTGATGTTGGAGTAGGAGGATTTATC
CTGATGACTTTAGGATACTGGTTCCACGGTAGGTACGATTATGCAAAGCAAAGAATTCTGGAGAGAACTGCCAGAGAAGG
AATTTAAAATGTGATTTAATATGAAAGTACTCTGATCCCGAAATAAGCCAACAGCAATAGCAGCAATGGA

Alignment

ORF - retro_opri_287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.49 %
• Parental protein coverage: 78.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTFKLLGILDVENTP-CARDSILYGSLGSAV-SGLGHFLFTSRIRRSCDVGVGGFILVTLGCWFHCRYNY
          KTF.LLGIL...NT..CAR.S.L.GSLGSA...GL.........RRSCDVGVGGFIL.TLG.WFH.RY.Y
Retrocopy KTFQLLGILGIKNTS<CARASVLNGSLGSAA<AGLELLC*LNLLRRSCDVGVGGFILMTLGYWFHGRYDY

Parental  AKQRIQERIAREGIKNKILYESTHLDPQRKHNKSSNG
          AKQRI.ER.AREGI.N.I.YEST.L.P......SSNG
Retrocopy AKQRILERTAREGI*NVI*YEST-LIPK*ANSNSSNG

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_287 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001381	4 retrocopies	retro_chof_1820, retro_chof_207, retro_chof_299, retro_chof_825,
Erinaceus europaeus	ENSEEUG00000012147	1 retrocopy	retro_eeur_104,
Homo sapiens	ENSG00000203667	1 retrocopy	retro_hsap_587,
Myotis lucifugus	ENSMLUG00000026132	7 retrocopies	retro_mluc_1273, retro_mluc_1505, retro_mluc_1863, retro_mluc_1954, retro_mluc_2343, retro_mluc_792, retro_mluc_958,
Monodelphis domestica	ENSMODG00000024669	1 retrocopy	retro_mdom_2014,
Mus musculus	ENSMUSG00000026500	1 retrocopy	retro_mmus_2957,
Nomascus leucogenys	ENSNLEG00000004027	1 retrocopy	retro_nleu_2518,
Ochotona princeps	ENSOPRG00000004534	6 retrocopies	retro_opri_1072, retro_opri_287 , retro_opri_31, retro_opri_585, retro_opri_676, retro_opri_720,
Pongo abelii	ENSPPYG00000000053	1 retrocopy	retro_pabe_2090,
Pteropus vampyrus	ENSPVAG00000002577	1 retrocopy	retro_pvam_945,
Rattus norvegicus	ENSRNOG00000004553	2 retrocopies	retro_rnor_1033, retro_rnor_2184,
Sorex araneus	ENSSARG00000004625	2 retrocopies	retro_sara_167, retro_sara_470,
Tupaia belangeri	ENSTBEG00000015272	4 retrocopies	retro_tbel_1186, retro_tbel_3207, retro_tbel_3838, retro_tbel_3926,
Tarsius syrichta	ENSTSYG00000005644	1 retrocopy	retro_tsyr_100,