RetrogeneDB ID: retro_opri_955

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_49611:5634..6123(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKP1
• Ensembl ID: ENSOPRG00000006637
• Aliases: None
• Description: S-phase kinase-associated protein 1 [Source:HGNC Symbol;Acc:10899]

Sequence

>retro_opri_955
ATGCCTTCAATTAAGTTGCAGAGTTCTGATGGAGAGACTTTTGAAGTTGATGTGGAAATTGCCAAGCAGTCTGTGACTAT
CGAGATCATTTAGAAAGATTTGGGAATGGATGATGAAGGAGATTATGACCCAGTTCCTCTACCAAATGTCAATGCAACAA
TATTTAAAAAGGGTATTCAGTGGTGCACCCACCACAAGGATGACCCCCACTCCTCCTGAAGATGATGAGAACAGATAAGC
GAACAGATGATATCCCTGTTTGGGACCAAGAATTTCTCAAAGTTGACCAACGAACACTTTTTGAGCTTATTTTGGCTGCA
AACTACTTAGACATCAAAGGTTTCTTTGATGTTATGCACAAGACTGTTGCCAACATGATCAAGGGAAAGACCCCTGAGGA
GATCCGCAAGACCTCCAATATAAAGAACAAACTTCACTGAAGCAGCAGCAGCCCAGGTACGCAAAGAGAACCAGTAGTGT
GAAGAGAAG

Alignment

ORF - retro_opri_955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDP-
          MPSIKLQSSDGE.FEVDVEIAKQSVTI.....DLGMDDEGD.DPVPLPNVNA.I.KK.IQWCTHHKDDP.
Retrocopy MPSIKLQSSDGETFEVDVEIAKQSVTIEII*KDLGMDDEGDYDPVPLPNVNATIFKKGIQWCTHHKDDP>

Parental  PPPEDDENK-EKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKT
          .PPE.D.....KRTDDIPVWDQEFLKVDQ.TLFELILAANYLDIKG..DV..KTVANMIKGKTPEEIRKT
Retrocopy TPPE-DDEN>DKRTDDIPVWDQEFLKVDQRTLFELILAANYLDIKGFFDVMHKTVANMIKGKTPEEIRKT

Parental  FNIKN-DFTEEEEAQVRKENQWCEEK
          .NIKN..FTE...AQVRKENQ.CEEK
Retrocopy SNIKN>NFTEAAAAQVRKENQ*CEEK

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_955 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 20 parental genes, and 120 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000994	5 retrocopies	retro_cfam_1613, retro_cfam_779, retro_cfam_813, retro_cfam_889, retro_cfam_965,
Callithrix jacchus	ENSCJAG00000013613	1 retrocopy	retro_cjac_112,
Cavia porcellus	ENSCPOG00000005164	8 retrocopies	retro_cpor_1038, retro_cpor_1133, retro_cpor_1345, retro_cpor_1446, retro_cpor_223, retro_cpor_243, retro_cpor_830, retro_cpor_832,
Dipodomys ordii	ENSDORG00000002912	3 retrocopies	retro_dord_338, retro_dord_512, retro_dord_720,
Equus caballus	ENSECAG00000003931	2 retrocopies	retro_ecab_466, retro_ecab_789,
Echinops telfairi	ENSETEG00000007560	5 retrocopies	retro_etel_1730, retro_etel_515, retro_etel_758, retro_etel_762, retro_etel_811,
Gorilla gorilla	ENSGGOG00000022930	7 retrocopies	retro_ggor_1288, retro_ggor_1300, retro_ggor_2601, retro_ggor_2602, retro_ggor_2796, retro_ggor_2797, retro_ggor_778,
Microcebus murinus	ENSMICG00000017588	3 retrocopies	retro_mmur_270, retro_mmur_803, retro_mmur_997,
Myotis lucifugus	ENSMLUG00000022919	13 retrocopies	retro_mluc_1455, retro_mluc_1738, retro_mluc_1895, retro_mluc_2009, retro_mluc_2260, retro_mluc_2261, retro_mluc_2520, retro_mluc_2527, retro_mluc_2557, retro_mluc_267, retro_mluc_383, retro_mluc_841, retro_mluc_944,
Macaca mulatta	ENSMMUG00000013046	7 retrocopies	retro_mmul_1171, retro_mmul_2082, retro_mmul_2091, retro_mmul_2508, retro_mmul_654, retro_mmul_795, retro_mmul_919,
Monodelphis domestica	ENSMODG00000014168	4 retrocopies	retro_mdom_1173, retro_mdom_155, retro_mdom_1648, retro_mdom_929,
Mus musculus	ENSMUSG00000036309	1 retrocopy	retro_mmus_2518,
Nomascus leucogenys	ENSNLEG00000008051	7 retrocopies	retro_nleu_1171, retro_nleu_1615, retro_nleu_1667, retro_nleu_2290, retro_nleu_323, retro_nleu_472, retro_nleu_827,
Ochotona princeps	ENSOPRG00000006637	7 retrocopies	retro_opri_1199, retro_opri_188, retro_opri_23, retro_opri_513, retro_opri_547, retro_opri_902, retro_opri_955 ,
Pongo abelii	ENSPPYG00000015783	7 retrocopies	retro_pabe_1915, retro_pabe_199, retro_pabe_2072, retro_pabe_2736, retro_pabe_2756, retro_pabe_626, retro_pabe_824,
Pteropus vampyrus	ENSPVAG00000012427	4 retrocopies	retro_pvam_1040, retro_pvam_1137, retro_pvam_1269, retro_pvam_503,
Sorex araneus	ENSSARG00000008307	4 retrocopies	retro_sara_241, retro_sara_446, retro_sara_492, retro_sara_609,
Tupaia belangeri	ENSTBEG00000015544	15 retrocopies	retro_tbel_1227, retro_tbel_1279, retro_tbel_1327, retro_tbel_1758, retro_tbel_1787, retro_tbel_1903, retro_tbel_1905, retro_tbel_240, retro_tbel_3024, retro_tbel_3267, retro_tbel_3848, retro_tbel_405, retro_tbel_4095, retro_tbel_528, retro_tbel_711,
Tarsius syrichta	ENSTSYG00000010696	11 retrocopies	retro_tsyr_1037, retro_tsyr_1370, retro_tsyr_1400, retro_tsyr_1896, retro_tsyr_1924, retro_tsyr_2058, retro_tsyr_210, retro_tsyr_336, retro_tsyr_396, retro_tsyr_464, retro_tsyr_762,
Tursiops truncatus	ENSTTRG00000016858	6 retrocopies	retro_ttru_1344, retro_ttru_1764, retro_ttru_1801, retro_ttru_656, retro_ttru_657, retro_ttru_961,