RetrogeneDB ID: retro_opri_1227

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_99972:298..753(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAN
• Ensembl ID: ENSOPRG00000002629
• Aliases: None
• Description: RAN, member RAS oncogene family [Source:HGNC Symbol;Acc:9846]

Sequence

>retro_opri_1227
GGGCCCATCAAGTTCAACCTCTGGGATAGAGTTAGCCAGAAGTTCGGTGGCCTGGAGAATGGCTAGTACATTCAAGCCCA
GTGTGTCGTCTTACTATTTGACATCACATCCAGAATTCTCTACAAGAATGTGCTTAACTGGCATAGAGACTTTATGTGCA
CCTATGAAAACATCCCCATTGTACTGTAAGGCAACAAGGTAGATGTTAAAGACAGGAAAGTGAAGGCAAAATCCATTATC
TTTGACCAAAAGAAGAACCTCTGGTACTACAATATTTCAAAGACTACAAATTTAAAAAGCCCTTCCTCTGGCTTGCTAGA
GAGTTCACTGGAGATCCCAAGTCAGAGTTCATTGCCATGCCCGCTCCTGCCTCACTAGAGGTGGTCATGGACTCAACACT
GTCAGTGCAGTATGAACATGACTTACAGGCTGTGCAGGCAACTACTACCCCAGAT

Alignment

ORF - retro_opri_1227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.77 %
• Parental protein coverage: 89.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSIKFNRLDTARQEKFGGLRGGSYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDI
          G.IKFN..D...Q.KFGGL..G.YIQAQC....FD.TSR..YKNV.NWHRD.....ENIPIVL.GNKVD.
Retrocopy GPIKFNLWDRVSQ-KFGGLENG*YIQAQCVVLLFDITSRILYKNVLNWHRDFMCTYENIPIVL*GNKVDV

Parental  KDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPAL-APPEVVMDPALAA
          KDRKVKAKSI.F..KKNL.YY.IS.....N...P...L.......P.......P.L.A..EVVMD..L..
Retrocopy KDRKVKAKSIIFDQKKNLWYYNISKTT--NLKSPSSGLLESSLEIPSQSSLPCPLL<ASLEVVMDSTLSV

Parental  QYEHDLEVAQTTALPD
          QYEHDL...Q.T..PD
Retrocopy QYEHDLQAVQATTTPD

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_1227 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 122 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004222	4 retrocopies	retro_amel_1119, retro_amel_1625, retro_amel_1631, retro_amel_700,
Canis familiaris	ENSCAFG00000006670	6 retrocopies	retro_cfam_1406, retro_cfam_1584, retro_cfam_1604, retro_cfam_2058, retro_cfam_426, retro_cfam_899,
Callithrix jacchus	ENSCJAG00000003927	8 retrocopies	retro_cjac_1558, retro_cjac_1844, retro_cjac_2509, retro_cjac_2952, retro_cjac_3071, retro_cjac_3107, retro_cjac_4222, retro_cjac_492,
Dasypus novemcinctus	ENSDNOG00000009230	12 retrocopies	retro_dnov_1154, retro_dnov_1269, retro_dnov_1485, retro_dnov_1543, retro_dnov_1585, retro_dnov_1795, retro_dnov_1924, retro_dnov_1945, retro_dnov_2142, retro_dnov_2189, retro_dnov_2613, retro_dnov_991,
Equus caballus	ENSECAG00000020532	3 retrocopies	retro_ecab_195, retro_ecab_591, retro_ecab_680,
Echinops telfairi	ENSETEG00000011875	18 retrocopies	retro_etel_1051, retro_etel_1161, retro_etel_1351, retro_etel_1365, retro_etel_1584, retro_etel_1673, retro_etel_1878, retro_etel_1896, retro_etel_1915, retro_etel_2141, retro_etel_2150, retro_etel_2189, retro_etel_294, retro_etel_383, retro_etel_409, retro_etel_412, retro_etel_514, retro_etel_813,
Felis catus	ENSFCAG00000027375	6 retrocopies	retro_fcat_1097, retro_fcat_1230, retro_fcat_1297, retro_fcat_1586, retro_fcat_1904, retro_fcat_269,
Gorilla gorilla	ENSGGOG00000015340	4 retrocopies	retro_ggor_2142, retro_ggor_2328, retro_ggor_2556, retro_ggor_3066,
Microcebus murinus	ENSMICG00000000653	4 retrocopies	retro_mmur_1270, retro_mmur_669, retro_mmur_791, retro_mmur_866,
Monodelphis domestica	ENSMODG00000015601	8 retrocopies	retro_mdom_100, retro_mdom_1718, retro_mdom_1990, retro_mdom_543, retro_mdom_580, retro_mdom_806, retro_mdom_814, retro_mdom_969,
Mustela putorius furo	ENSMPUG00000004044	6 retrocopies	retro_mputfur_1190, retro_mputfur_1523, retro_mputfur_228, retro_mputfur_755, retro_mputfur_784, retro_mputfur_899,
Mus musculus	ENSMUSG00000029430	4 retrocopies	retro_mmus_1653, retro_mmus_182, retro_mmus_2029, retro_mmus_265,
Nomascus leucogenys	ENSNLEG00000008282	4 retrocopies	retro_nleu_1565, retro_nleu_2303, retro_nleu_2353, retro_nleu_775,
Ornithorhynchus anatinus	ENSOANG00000006447	1 retrocopy	retro_oana_62,
Oryctolagus cuniculus	ENSOCUG00000026506	2 retrocopies	retro_ocun_1139, retro_ocun_958,
Ochotona princeps	ENSOPRG00000002629	7 retrocopies	retro_opri_1062, retro_opri_1227 , retro_opri_514, retro_opri_622, retro_opri_647, retro_opri_74, retro_opri_97,
Pteropus vampyrus	ENSPVAG00000014742	15 retrocopies	retro_pvam_1023, retro_pvam_1049, retro_pvam_1328, retro_pvam_365, retro_pvam_485, retro_pvam_597, retro_pvam_61, retro_pvam_746, retro_pvam_770, retro_pvam_863, retro_pvam_933, retro_pvam_934, retro_pvam_935, retro_pvam_948, retro_pvam_968,
Rattus norvegicus	ENSRNOG00000000938	3 retrocopies	retro_rnor_138, retro_rnor_410, retro_rnor_917,
Sarcophilus harrisii	ENSSHAG00000018018	1 retrocopy	retro_shar_538,
Ictidomys tridecemlineatus	ENSSTOG00000003992	3 retrocopies	retro_itri_1009, retro_itri_1442, retro_itri_723,
Vicugna pacos	ENSVPAG00000008880	3 retrocopies	retro_vpac_436, retro_vpac_589, retro_vpac_85,