RetrogeneDB ID: retro_opri_924

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_462:241173..241889(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAB
• Ensembl ID: ENSOPRG00000011836
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide [Source:HGNC Symbol;Acc:12849]

Sequence

>retro_opri_924
ATGGAGAGAGCCCATCTGATCCAGAAGGCCAAGTTGGCCGAGCAGGCTGAGCGCTACGAGGACATGGCAGGCTTCATGAA
GGGTGCCGTGGAAAAGGGCGAGGAGCTTTCCTGTGAGGAGCGAAACCTGCTCTCAGTGGCCTACAAGAACGTCGTGGGCG
GCCAGAGGGCTGCCTGGAGGGTCCTGTCTAGCATTGAGCAGAAAAGCACCGAGGAAGGCTCAGAAGAGCAGGGCCCCGAA
GTGCGTGAGTACCGGGAGAAGGTGGAGACGGAGCTCCGGGGTGTGTGCGACACCGTGCTGGGCCTGCTGGACACCCACCT
CATCAAGGAGGCCGGCGACGCCGAGAGCCGGGTCTTCTACCTGAAGATGAAGGGAGACTACTACCGCTACCTGGCCGAGG
TGGCCACCGGCGATGACAAGAAACGCATCATCGACTCCGCCCGGTCGGCCTACCAGGAGGCCATGGACATCAGCAAGAAG
GAGATGCCGCCCACCAACCCCATCCGCCTGGGCCTGGCCCTGAACTTTTCCGTCTTCCACTATGAGATTGCCAACAGCCC
CGAGGAGGCCATCACGCTGGCCAAGACCACTTTCGACGAAGCCATGGCTGACCTGCACACCCTCAGCGAGTACTCCTACA
AAGACAGCACCCTCATCATGCAGCTGCTGCGAGACAACCTGACGCTGTGACAGCCGACAACGCCGGAGAAGAGGGC

Alignment

ORF - retro_opri_924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.25 %
• Parental protein coverage: 96.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKT-
          M....L.QKAKLAEQAERY.DMA..MK...E.G.ELS.EERNLLSVAYKNVVG..R..WRV.SSIEQK..
Retrocopy MERAHLIQKAKLAEQAERYEDMAGFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKST

Parental  -ERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLILNATQPESKVFYLKMKGDYFRYLSEVASGDNK
          .E..E.......EYREK.E.EL...C..VL.LLD..LI..A...ES.VFYLKMKGDY.RYL.EVA.GD.K
Retrocopy EEGSEEQGPEVREYREKVETELRGVCDTVLGLLDTHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDK

Parental  QTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNE
          .........AYQEA..ISKKEM.PT.PIRLGLALNFSVF.YEI.NSPE.A..LAKT.FDEA.A.L.TL.E
Retrocopy KRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAITLAKTTFDEAMADLHTLSE

Parental  ESYKDSTLIMQLLRDNLTL-WTSENQGDEG
          .SYKDSTLIMQLLRDNLTL..T..N.G.EG
Retrocopy YSYKDSTLIMQLLRDNLTL<VTADNAGEEG

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_924 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 26 parental genes, and 142 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011796	1 retrocopy	retro_acar_8,
Choloepus hoffmanni	ENSCHOG00000005782	15 retrocopies	retro_chof_1049, retro_chof_1325, retro_chof_1630, retro_chof_1670, retro_chof_1975, retro_chof_22, retro_chof_2221, retro_chof_2350, retro_chof_2423, retro_chof_2619, retro_chof_326, retro_chof_352, retro_chof_487, retro_chof_707, retro_chof_971,
Callithrix jacchus	ENSCJAG00000017664	2 retrocopies	retro_cjac_1002, retro_cjac_2214,
Dipodomys ordii	ENSDORG00000001064	14 retrocopies	retro_dord_235, retro_dord_236, retro_dord_255, retro_dord_256, retro_dord_258, retro_dord_259, retro_dord_262, retro_dord_263, retro_dord_332, retro_dord_442, retro_dord_545, retro_dord_681, retro_dord_725, retro_dord_9,
Echinops telfairi	ENSETEG00000009967	4 retrocopies	retro_etel_1221, retro_etel_1380, retro_etel_1536, retro_etel_1705,
Homo sapiens	ENSG00000166913	4 retrocopies	retro_hsap_4160, retro_hsap_4841, retro_hsap_622, retro_hsap_855,
Gorilla gorilla	ENSGGOG00000004580	2 retrocopies	retro_ggor_2795, retro_ggor_699,
Microcebus murinus	ENSMICG00000000973	7 retrocopies	retro_mmur_1044, retro_mmur_1100, retro_mmur_1288, retro_mmur_1576, retro_mmur_27, retro_mmur_305, retro_mmur_979,
Myotis lucifugus	ENSMLUG00000006319	1 retrocopy	retro_mluc_871,
Macaca mulatta	ENSMMUG00000013206	3 retrocopies	retro_mmul_1061, retro_mmul_236, retro_mmul_673,
Monodelphis domestica	ENSMODG00000016200	2 retrocopies	retro_mdom_1557, retro_mdom_212,
Nomascus leucogenys	ENSNLEG00000006643	2 retrocopies	retro_nleu_42, retro_nleu_422,
Oryctolagus cuniculus	ENSOCUG00000003002	1 retrocopy	retro_ocun_273,
Otolemur garnettii	ENSOGAG00000008909	3 retrocopies	retro_ogar_122, retro_ogar_1243, retro_ogar_2934,
Ochotona princeps	ENSOPRG00000000276	3 retrocopies	retro_opri_1218, retro_opri_218, retro_opri_967,
Ochotona princeps	ENSOPRG00000011836	2 retrocopies	retro_opri_56, retro_opri_924 ,
Pongo abelii	ENSPPYG00000011041	5 retrocopies	retro_pabe_3453, retro_pabe_3454, retro_pabe_3519, retro_pabe_3520, retro_pabe_692,
Pan troglodytes	ENSPTRG00000013529	12 retrocopies	retro_ptro_1010, retro_ptro_1686, retro_ptro_2390, retro_ptro_2828, retro_ptro_2887, retro_ptro_3125, retro_ptro_3201, retro_ptro_3225, retro_ptro_412, retro_ptro_453, retro_ptro_594, retro_ptro_965,
Pteropus vampyrus	ENSPVAG00000012662	1 retrocopy	retro_pvam_157,
Sarcophilus harrisii	ENSSHAG00000011241	1 retrocopy	retro_shar_483,
Sus scrofa	ENSSSCG00000007381	1 retrocopy	retro_sscr_506,
Ictidomys tridecemlineatus	ENSSTOG00000003733	1 retrocopy	retro_itri_1214,
Tupaia belangeri	ENSTBEG00000002806	47 retrocopies	retro_tbel_1038, retro_tbel_1272, retro_tbel_1460, retro_tbel_1472, retro_tbel_1572, retro_tbel_1653, retro_tbel_1664, retro_tbel_2127, retro_tbel_2128, retro_tbel_2229, retro_tbel_2246, retro_tbel_228, retro_tbel_2371, retro_tbel_2373, retro_tbel_2379, retro_tbel_2397, retro_tbel_2512, retro_tbel_2536, retro_tbel_2540, retro_tbel_2542, retro_tbel_2583, retro_tbel_2584, retro_tbel_2615, retro_tbel_2617, retro_tbel_3502, retro_tbel_3554, retro_tbel_3604, retro_tbel_3642, retro_tbel_3743, retro_tbel_390, retro_tbel_3989, retro_tbel_3993, retro_tbel_40, retro_tbel_4101, retro_tbel_4121, retro_tbel_4338, retro_tbel_4447, retro_tbel_4456, retro_tbel_4459, retro_tbel_4510, retro_tbel_4514, retro_tbel_4604, retro_tbel_4664, retro_tbel_4690, retro_tbel_5, retro_tbel_705, retro_tbel_854,
Tarsius syrichta	ENSTSYG00000006537	4 retrocopies	retro_tsyr_1065, retro_tsyr_1473, retro_tsyr_1637, retro_tsyr_2084,
Tursiops truncatus	ENSTTRG00000007615	1 retrocopy	retro_ttru_762,
Vicugna pacos	ENSVPAG00000005023	3 retrocopies	retro_vpac_396, retro_vpac_516, retro_vpac_9,