RetrogeneDB ID: retro_opri_590

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1840:9255..9834(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOA
• Ensembl ID: ENSOPRG00000009638
• Aliases: None
• Description: ras homolog family member A [Source:HGNC Symbol;Acc:667]

Sequence

>retro_opri_590
ATGGCTGCCCTCCGCAAGAAGCTGGTGGTCGTGGGGGCCGGCGCTTGCGGCAAGACGAGCCTGCTGGTGGTGTTCAGCCG
CGACTCCTTCCCGGAGGAGTACGTGCCCACCGTGTTTGAGAACTACGTGGCCGACGTGGAGGTGGACGGGAAGCGTGTGG
AGCTGGCCCTGTGGGACACAGCGGGCCAGGAGGAGTACGACCGCCTGCGGCCCCTGTCTTACCCGGACACCGACGTCATC
CTCATGTGCTTCTCCATCAGCAGTCCCGACAGTCTGGAAAACATCCCGGTCAAGTGGGCGCCCGAGGTGCGGCACTTCTG
CCCCAGCGTGCCCATCGTCCTGGTGGGCAACAAGAAGGATCTCCGCCACGATGAGGGCACCAGGCGGGCGCTGGCGGCCT
GGAAGCAGGAGCCGGTGAGGCCCGAGGCAGGCAGGGACATGGCCGGCAGGGTCGGCGCCTTCGGGTACCTGGAGTGCTCC
GCCAAGACCAAGGAGGGCGTGAGGGAGGTGTTCGAGCTGGCCACGCGAGCCGCCCTGCAGGCCAGGCGTGGCAGGAAGCG
CTGGCGGTGCCTGGTCCTG

Alignment

ORF - retro_opri_590 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
          MAA.RKKLV.VG.GACGKT.LL.VFS.D.FPE.YVPTVFENYVAD.EVDGK.VELALWDTAGQE.YDRLR
Retrocopy MAALRKKLVVVGAGACGKTSLLVVFSRDSFPEEYVPTVFENYVADVEVDGKRVELALWDTAGQEEYDRLR

Parental  PLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVK
          PLSYPDTDVILMCFSI.SPDSLENIP.KW.PEV.HFCP.VPI.LVGNKKDLR.DE.TRR.LA..KQEPV.
Retrocopy PLSYPDTDVILMCFSISSPDSLENIPVKWAPEVRHFCPSVPIVLVGNKKDLRHDEGTRRALAAWKQEPVR

Parental  PEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGCLVL
          PE.GRDMA.R.GAFGY.ECSAKTK.GVREVFE.ATRAALQARRG.K...CLVL
Retrocopy PEAGRDMAGRVGAFGYLECSAKTKEGVREVFELATRAALQARRGRKRWRCLVL

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_590 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 24 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008297	1 retrocopy	retro_acar_41,
Anas platyrhynchos	ENSAPLG00000014687	1 retrocopy	retro_apla_10,
Canis familiaris	ENSCAFG00000023066	2 retrocopies	retro_cfam_1652, retro_cfam_186,
Callithrix jacchus	ENSCJAG00000003904	3 retrocopies	retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Cavia porcellus	ENSCPOG00000014073	1 retrocopy	retro_cpor_514,
Dipodomys ordii	ENSDORG00000003382	3 retrocopies	retro_dord_1, retro_dord_18, retro_dord_538,
Homo sapiens	ENSG00000067560	2 retrocopies	retro_hsap_108, retro_hsap_3632,
Gasterosteus aculeatus	ENSGACG00000005670	1 retrocopy	retro_gacu_9,
Gallus gallus	ENSGALG00000003806	1 retrocopy	retro_ggal_5,
Gadus morhua	ENSGMOG00000008188	1 retrocopy	retro_gmor_18,
Latimeria chalumnae	ENSLACG00000016941	1 retrocopy	retro_lcha_15,
Meleagris gallopavo	ENSMGAG00000002280	1 retrocopy	retro_mgal_2,
Macaca mulatta	ENSMMUG00000012962	1 retrocopy	retro_mmul_977,
Monodelphis domestica	ENSMODG00000012981	2 retrocopies	retro_mdom_19, retro_mdom_294,
Mustela putorius furo	ENSMPUG00000013840	5 retrocopies	retro_mputfur_1015, retro_mputfur_140, retro_mputfur_1541, retro_mputfur_1588, retro_mputfur_650,
Mus musculus	ENSMUSG00000007815	9 retrocopies	retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,
Ornithorhynchus anatinus	ENSOANG00000013807	1 retrocopy	retro_oana_7,
Oreochromis niloticus	ENSONIG00000018884	1 retrocopy	retro_onil_32,
Ochotona princeps	ENSOPRG00000009638	1 retrocopy	retro_opri_590 ,
Pelodiscus sinensis	ENSPSIG00000015328	1 retrocopy	retro_psin_7,
Rattus norvegicus	ENSRNOG00000050519	3 retrocopies	retro_rnor_127, retro_rnor_2899, retro_rnor_408,
Ictidomys tridecemlineatus	ENSSTOG00000004561	2 retrocopies	retro_itri_39, retro_itri_96,
Takifugu rubripes	ENSTRUG00000011944	1 retrocopy	retro_trub_19,
Tursiops truncatus	ENSTTRG00000017370	2 retrocopies	retro_ttru_27, retro_ttru_339,