RetrogeneDB ID: retro_opri_135

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2662:2957..3351(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000011793
• Aliases: None
• Description: None

Sequence

>retro_opri_135
GCAGAGTGCGGACACAGTTTTTCGCTGACTACATTCAGCCCCTCCGGTAAACTTGTCCAGATTGAATATGCTGTGGCTGG
AGGAGCCCCTTCAGTGGGAATTAAAGGTACCAATGGTGTCGTGTTAGCAAAGAGAAGAAACAGAAATCCATTGTGTATGA
TGAGTGCAGTGTGCACAAGGTGGAGCCTATCGCCAAGCACATAGGCTTGGTGTACAGCGGCATGGGCACTGCTACAGAGT
GCTGGTACACAGAGCTCGGAAGCTTGCCCAGCAGTATCTGATTTACCAGGAATCCAGCCCCACAGCTCAGCTGGTGCAGG
TAGTGGCATCGGTGATGCAGGAGTACACCCACTCAGGTGGTGTTCATCCTTTTGGAGTTTCTTTACTTATTTGT

Alignment

ORF - retro_opri_135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.06 %
• Parental protein coverage: 58.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLAT-EKKQKSILYDERSVHKVEPITK
          AE.G.SFSLTTFSPSGKLVQIEY...AVAGGAPSVGIK..NGVVLA..EKKQKSI.YDE.SVHKVEPI.K
Retrocopy AECGHSFSLTTFSPSGKLVQIEY---AVAGGAPSVGIKGTNGVVLAK<EKKQKSIVYDECSVHKVEPIAK

Parental  HIGLVYSGMGPD-YRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLIC
          HIGLVYSGMG...YRVLVHRARKLAQQY.L.YQE..PTAQLVQ.VASVMQEYT.SGGV.PFGVSLLIC
Retrocopy HIGLVYSGMGTA<YRVLVHRARKLAQQY-LIYQESSPTAQLVQVVASVMQEYTHSGGVHPFGVSLLIC

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_135 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 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000990	3 retrocopies	retro_btau_296, retro_btau_384, retro_btau_889,
Choloepus hoffmanni	ENSCHOG00000000644	1 retrocopy	retro_chof_893,
Callithrix jacchus	ENSCJAG00000007730	4 retrocopies	retro_cjac_1096, retro_cjac_1868, retro_cjac_2583, retro_cjac_852,
Cavia porcellus	ENSCPOG00000013134	1 retrocopy	retro_cpor_1512,
Dasypus novemcinctus	ENSDNOG00000011910	2 retrocopies	retro_dnov_2202, retro_dnov_724,
Echinops telfairi	ENSETEG00000015835	2 retrocopies	retro_etel_1569, retro_etel_2022,
Homo sapiens	ENSG00000106588	2 retrocopies	retro_hsap_2199, retro_hsap_908,
Gorilla gorilla	ENSGGOG00000006538	1 retrocopy	retro_ggor_735,
Myotis lucifugus	ENSMLUG00000010086	2 retrocopies	retro_mluc_1050, retro_mluc_135,
Macaca mulatta	ENSMMUG00000022451	2 retrocopies	retro_mmul_1114, retro_mmul_923,
Nomascus leucogenys	ENSNLEG00000003177	1 retrocopy	retro_nleu_329,
Oryctolagus cuniculus	ENSOCUG00000012092	1 retrocopy	retro_ocun_774,
Ochotona princeps	ENSOPRG00000011793	2 retrocopies	retro_opri_135 , retro_opri_791,
Pongo abelii	ENSPPYG00000017612	2 retrocopies	retro_pabe_2076, retro_pabe_783,
Pan troglodytes	ENSPTRG00000019120	2 retrocopies	retro_ptro_1670, retro_ptro_628,
Ictidomys tridecemlineatus	ENSSTOG00000013334	1 retrocopy	retro_itri_223,
Tarsius syrichta	ENSTSYG00000014299	2 retrocopies	retro_tsyr_132, retro_tsyr_246,
Tursiops truncatus	ENSTTRG00000005649	1 retrocopy	retro_ttru_356,