RetrogeneDB ID: retro_opri_900

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_4269:56253..56709(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL24
• Ensembl ID: ENSOPRG00000004255
• Aliases: None
• Description: ribosomal protein L24 [Source:HGNC Symbol;Acc:10325]

Sequence

>retro_opri_900
TCCCTTCGCCATCTTTCCTCTTCCAGGGGAGCCGCCGCCATGAAGATTGAATTCTGCAGTTTCAGTGGGCACAAGATCTA
TCCCGGACACGGGGAGACGCTACGCCAGAACCGACGGGAAGGTTTTCCAGTTTCTTAACGCAAAATGCGAGTTTGCGTTT
CTTTCCAAGAGGAATCTGCAGCAGATCAGTTGGGCTGTCCTCTACTGAAGGAAACACAAAAAGGGGCAGTCAGAAGAAAT
TCAAAAGAAAAGAACTCGTCGTGCAAATTCTAGAGAGCCGTCATTGGTGCGCCTCTTGCTGATACCGTGGCCAAGAGAAA
TCAGAAGCCTGAAGTTAGGAAGGCTCAACGAGAACAAGCGGTCAGCGCTGCCAAGGAAGCCAAACAGGCTACGCAGACGT
CTAAAAAGACAGCAATGCCTGCTGCTAAGGCTCTTGCAAAAGCAGCGCCTAAGCAA

Alignment

ORF - retro_opri_900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 88.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLRHLSSSRGAAAMKVELCSFSGYKIYPGHG-RRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYR
          SLRHLSSSRGAAAMK.E.CSFSG.KIYPGHG.RRYARTDGKVFQFLNAKCE.AFLSKRN..QI.W.VLY.
Retrocopy SLRHLSSSRGAAAMKIEFCSFSGHKIYPGHG>RRYARTDGKVFQFLNAKCEFAFLSKRNLQQISWAVLY*

Parental  RKHKKGQSEEIQKKRTRR-AVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKT
          RKHKKGQSEEI..K...R...KF.RA..GA.LAD..AKRNQKPEVRKAQREQA..AAKEAK.A.Q.SKKT
Retrocopy RKHKKGQSEEI-QKKRTR<SCKF*RAVIGAPLADTVAKRNQKPEVRKAQREQAVSAAKEAKQATQTSKKT

Parental  AMAAAKAPTKAAPKQ
          AM.AAKA..KAAPKQ
Retrocopy AMPAAKALAKAAPKQ

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_900 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 25 parental genes, and 162 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013461	1 retrocopy	retro_btau_1143,
Callithrix jacchus	ENSCJAG00000000496	3 retrocopies	retro_cjac_2544, retro_cjac_2941, retro_cjac_327,
Cavia porcellus	ENSCPOG00000019941	5 retrocopies	retro_cpor_1020, retro_cpor_461, retro_cpor_474, retro_cpor_904, retro_cpor_947,
Dasypus novemcinctus	ENSDNOG00000003194	9 retrocopies	retro_dnov_1209, retro_dnov_1259, retro_dnov_1449, retro_dnov_1643, retro_dnov_2191, retro_dnov_2407, retro_dnov_2537, retro_dnov_523, retro_dnov_657,
Erinaceus europaeus	ENSEEUG00000009320	3 retrocopies	retro_eeur_505, retro_eeur_534, retro_eeur_621,
Felis catus	ENSFCAG00000003327	1 retrocopy	retro_fcat_31,
Homo sapiens	ENSG00000114391	8 retrocopies	retro_hsap_1437, retro_hsap_1752, retro_hsap_2418, retro_hsap_2614, retro_hsap_2743, retro_hsap_281, retro_hsap_3583, retro_hsap_4179,
Gorilla gorilla	ENSGGOG00000011609	8 retrocopies	retro_ggor_1106, retro_ggor_1504, retro_ggor_1831, retro_ggor_1909, retro_ggor_2252, retro_ggor_2417, retro_ggor_2803, retro_ggor_324,
Macropus eugenii	ENSMEUG00000009177	7 retrocopies	retro_meug_1769, retro_meug_371, retro_meug_385, retro_meug_449, retro_meug_730, retro_meug_759, retro_meug_963,
Myotis lucifugus	ENSMLUG00000017005	4 retrocopies	retro_mluc_1990, retro_mluc_2185, retro_mluc_35, retro_mluc_393,
Macaca mulatta	ENSMMUG00000015059	9 retrocopies	retro_mmul_1234, retro_mmul_1711, retro_mmul_1803, retro_mmul_2263, retro_mmul_2521, retro_mmul_37, retro_mmul_560, retro_mmul_609, retro_mmul_823,
Monodelphis domestica	ENSMODG00000001916	3 retrocopies	retro_mdom_675, retro_mdom_854, retro_mdom_974,
Nomascus leucogenys	ENSNLEG00000003276	6 retrocopies	retro_nleu_1413, retro_nleu_1790, retro_nleu_1894, retro_nleu_2031, retro_nleu_2815, retro_nleu_2937,
Oryctolagus cuniculus	ENSOCUG00000000791	8 retrocopies	retro_ocun_1401, retro_ocun_190, retro_ocun_303, retro_ocun_323, retro_ocun_420, retro_ocun_480, retro_ocun_526, retro_ocun_531,
Ochotona princeps	ENSOPRG00000004255	6 retrocopies	retro_opri_1100, retro_opri_1109, retro_opri_1131, retro_opri_900 , retro_opri_918, retro_opri_95,
Procavia capensis	ENSPCAG00000005918	1 retrocopy	retro_pcap_192,
Pongo abelii	ENSPPYG00000013588	6 retrocopies	retro_pabe_1191, retro_pabe_1450, retro_pabe_1782, retro_pabe_2277, retro_pabe_2343, retro_pabe_3419,
Pan troglodytes	ENSPTRG00000015176	2 retrocopies	retro_ptro_1214, retro_ptro_85,
Pteropus vampyrus	ENSPVAG00000009889	3 retrocopies	retro_pvam_1317, retro_pvam_743, retro_pvam_831,
Rattus norvegicus	ENSRNOG00000001611	25 retrocopies	retro_rnor_1244, retro_rnor_1245, retro_rnor_1247, retro_rnor_1248, retro_rnor_1250, retro_rnor_1251, retro_rnor_1252, retro_rnor_1253, retro_rnor_1452, retro_rnor_1643, retro_rnor_1699, retro_rnor_1850, retro_rnor_1851, retro_rnor_1985, retro_rnor_2026, retro_rnor_2134, retro_rnor_2148, retro_rnor_2205, retro_rnor_2214, retro_rnor_2294, retro_rnor_2709, retro_rnor_435, retro_rnor_751, retro_rnor_964, retro_rnor_993,
Sorex araneus	ENSSARG00000007615	6 retrocopies	retro_sara_198, retro_sara_204, retro_sara_330, retro_sara_535, retro_sara_574, retro_sara_711,
Sarcophilus harrisii	ENSSHAG00000008226	2 retrocopies	retro_shar_171, retro_shar_264,
Ictidomys tridecemlineatus	ENSSTOG00000014654	2 retrocopies	retro_itri_442, retro_itri_69,
Tupaia belangeri	ENSTBEG00000012044	30 retrocopies	retro_tbel_1349, retro_tbel_1429, retro_tbel_1676, retro_tbel_2076, retro_tbel_2248, retro_tbel_2553, retro_tbel_2836, retro_tbel_2853, retro_tbel_2931, retro_tbel_3363, retro_tbel_3507, retro_tbel_3544, retro_tbel_3552, retro_tbel_3557, retro_tbel_3634, retro_tbel_3636, retro_tbel_3664, retro_tbel_4105, retro_tbel_4114, retro_tbel_4139, retro_tbel_4236, retro_tbel_4237, retro_tbel_431, retro_tbel_4677, retro_tbel_569, retro_tbel_607, retro_tbel_678, retro_tbel_700, retro_tbel_73, retro_tbel_779,
Tarsius syrichta	ENSTSYG00000002314	4 retrocopies	retro_tsyr_266, retro_tsyr_285, retro_tsyr_401, retro_tsyr_460,