RetrogeneDB ID: retro_opri_12

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_87160:4240..4630(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000000888
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000000983
• Aliases: None
• Description: None

Sequence

>retro_opri_12
ATGGCCGAGCTGATCCAGAAGAAGCTGCAGGGAGAAGTGGAGAAGTACCAACAGCTACAGAAGGACTTGAGTAAATCCAT
GTCAGGGAGACAGAAGCTGGAAGCACAGTTAACAGAAAACAACATCGTGAAGGAGGAACTGGCTCTACTGGATGGATCCA
ACGTGGTCTTCAAACTTCTGGGCCCCGTGCTGGTTAAGCAGGAGCTGGGGGAGGCGCGGGCCACCGTGGGCAAGAGGCTG
GACTACATCACTGCTGAAATTAAGCGATACGAATCCCAGCTCCGGGACCTGGAGCGGCAGTCGGAGCAGCAGAGGGAAAC
CCTTGCCCAGCTGCAGCAGGAGTTCCAGCGGGCCCAGGCAGCAAAGGCAGGAGCACCTGGGAAAGCCTGA

Alignment

ORF - retro_opri_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG
          MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG
Retrocopy MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG

Parental  EARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKAGAPGKA
          EARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKAGAPGKA
Retrocopy EARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKAGAPGKA

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_12 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 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Canis familiaris	ENSCAFG00000000956	2 retrocopies	retro_cfam_1749, retro_cfam_1981,
Cavia porcellus	ENSCPOG00000019520	1 retrocopy	retro_cpor_570,
Dasypus novemcinctus	ENSDNOG00000011211	2 retrocopies	retro_dnov_1317, retro_dnov_2064,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Felis catus	ENSFCAG00000028199	1 retrocopy	retro_fcat_1784,
Loxodonta africana	ENSLAFG00000012967	1 retrocopy	retro_lafr_363,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mustela putorius furo	ENSMPUG00000002364	1 retrocopy	retro_mputfur_608,
Mus musculus	ENSMUSG00000024309	1 retrocopy	retro_mmus_1930,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12 ,
Procavia capensis	ENSPCAG00000006019	1 retrocopy	retro_pcap_226,
Pteropus vampyrus	ENSPVAG00000001910	1 retrocopy	retro_pvam_391,
Rattus norvegicus	ENSRNOG00000000473	2 retrocopies	retro_rnor_2216, retro_rnor_2869,
Sorex araneus	ENSSARG00000006330	2 retrocopies	retro_sara_338, retro_sara_453,
Tupaia belangeri	ENSTBEG00000013280	1 retrocopy	retro_tbel_454,