RetrogeneDB ID: retro_opri_2

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5896:131371..131803(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000005800
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RRAS2
• Ensembl ID: ENSOPRG00000005967
• Aliases: None
• Description: related RAS viral (r-ras) oncogene homolog 2 [Source:HGNC Symbol;Acc:17271]

Sequence

>retro_opri_2
CTGGACACGGCCAGGCAAGAGGAGTTCAGCGCCATGCGGGAGCAGTACATGCGCATGGGGGATGGCTTCCTCATCGTCTT
CTCCGTCACAGACAAGGCCAGCTTTGAGCACGTGGACCGCTTCCACCAGCTCATCCTCCGTGTCAAGGACAGGGAGTCAT
TCCTGATGATCCTCGTGGCCAAAAAGGTGGATCTGATGCACTTGAGGAAAATCACCAGGGAGCAGGGCAAGGAGATGGCG
GCCAAACACAATATTCCATACATAGAGACCAGCGCCCAGGACCCCCCTCTCAATGTGAACAAAGCCTTCCATGACCTCGT
TAGAGTAATCAGGCAACAGATTCCGGAAAAAAGCCAGAAGGAGAAGAAGAAAACTAAATGGCGGGGAGACCGGGCCACTG
GCACCCACAAACTGCAGTGCGTGATTTTGTGA

Alignment

ORF - retro_opri_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.88 %
• Parental protein coverage: 95.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDTAGQEEFGAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQ
          LDTA.QEEF.AMREQYMR.G.GFL.VFSVTD..SFE....F...ILRVKDR..F.MIL...K.DL.H.R.
Retrocopy LDTARQEEFSAMREQYMRMGDGFLIVFSVTDKASFEHVDRFHQLILRVKDRESFLMILVAKKVDLMHLRK

Parental  VTQEEGQQLARQLKVTYMEASAK-IRMNVDQAFHELVRVIRKFQEQECPPSPEPTRKEKDKKG
          .T.E.G...A......Y.E.SA.....NV..AFH.LVRVIR....Q..P.......K.....G
Retrocopy ITREQGKEMAAKHNIPYIETSAQDPPLNVNKAFHDLVRVIR----QQIPEKSQKEKKKTKWRG

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_2 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 21 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002367	1 retrocopy	retro_amel_947,
Bos taurus	ENSBTAG00000011905	1 retrocopy	retro_btau_1295,
Choloepus hoffmanni	ENSCHOG00000003135	7 retrocopies	retro_chof_111, retro_chof_1639, retro_chof_2065, retro_chof_2644, retro_chof_2706, retro_chof_389, retro_chof_521,
Dasypus novemcinctus	ENSDNOG00000011828	6 retrocopies	retro_dnov_124, retro_dnov_1458, retro_dnov_1708, retro_dnov_1779, retro_dnov_2331, retro_dnov_988,
Erinaceus europaeus	ENSEEUG00000000240	1 retrocopy	retro_eeur_531,
Felis catus	ENSFCAG00000009578	1 retrocopy	retro_fcat_386,
Homo sapiens	ENSG00000133818	1 retrocopy	retro_hsap_390,
Gorilla gorilla	ENSGGOG00000004759	1 retrocopy	retro_ggor_1813,
Myotis lucifugus	ENSMLUG00000007005	1 retrocopy	retro_mluc_1264,
Macaca mulatta	ENSMMUG00000000664	2 retrocopies	retro_mmul_1604, retro_mmul_965,
Monodelphis domestica	ENSMODG00000028397	2 retrocopies	retro_mdom_1254, retro_mdom_577,
Oryctolagus cuniculus	ENSOCUG00000011362	1 retrocopy	retro_ocun_1645,
Otolemur garnettii	ENSOGAG00000027655	1 retrocopy	retro_ogar_1081,
Ochotona princeps	ENSOPRG00000005967	1 retrocopy	retro_opri_2 ,
Pongo abelii	ENSPPYG00000025912	1 retrocopy	retro_pabe_3043,
Pan troglodytes	ENSPTRG00000003383	2 retrocopies	retro_ptro_1747, retro_ptro_301,
Rattus norvegicus	ENSRNOG00000012258	1 retrocopy	retro_rnor_750,
Ictidomys tridecemlineatus	ENSSTOG00000022169	1 retrocopy	retro_itri_1457,
Tupaia belangeri	ENSTBEG00000001292	1 retrocopy	retro_tbel_3234,
Tursiops truncatus	ENSTTRG00000010419	1 retrocopy	retro_ttru_1218,
Vicugna pacos	ENSVPAG00000008814	1 retrocopy	retro_vpac_165,