RetrogeneDB ID: retro_opri_33

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_116:188680..189227(+)
• Located in intron of: ENSOPRG00000006224

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6
• Ensembl ID: ENSOPRG00000000751
• Aliases: None
• Description: ribosomal protein S6 [Source:HGNC Symbol;Acc:10429]

Sequence

>retro_opri_33
GGCTTCCCCATGAAGCAAGGAGTCTTGACCCATGGCCAGGTTTGCCTGCTGCTGAGTAAGGAGCACTGCTGTTACAGGCT
GTGCAGAACTGGAGAAAGAAAAGTGCAAATCTGTTCGGGGCTGCACTGTTGATGCCAACTTCAGTGTTCTCAACATGATT
AATATAAAATAAGGAGAGAAAGGCATTCCTGTATTGACTGATACCACAGTGTTTAATCACTTGGGTTCTGACAGGGCCTG
CAGATTCTGCAAACTTTTAGAACTCTCTAAAGATGATGTACACCAGCATGCTGTAAGAAAGCCTCTAAACAAAGAAGGTA
AGAAACCTAGGACCCAAACACTCAAGATTCAGCATCTTGTCACTTCACAAGTCTTCCAGCACAAATGCCAGCACATTGCT
CTGAAGAAACACTGTAACAAGGAAGTGGCTGCAGAATATGCTAAACTTTTGACCAAGAGGATGGAGGCCAAAGAAAAATG
CCAAGAACAGAGTGTTAAGAAACATGGGATGTCTTCTCTGAGAGCATCTACTTCTAAATCAGTCCAG

Alignment

ORF - retro_opri_33 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 75.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFPMKQGVLT-GRV-RLLSKGHSC-RPRRTGERKR-KSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTT
          GFPMKQGVLT.G.V..LLSK.H.C.R..RTGERK..KSVRGC.VDAN.SVLN....K.GEK.IP.LTDTT
Retrocopy GFPMKQGVLTHGQVCLLLSKEHCCYRLCRTGERKV>KSVRGCTVDANFSVLNMINIK*GEKGIPVLTDTT

Parental  VPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQR
          V...LG..RA.R..KL..LSK.DDV.Q..VRKPLNKEGKKPRT...KIQ.LVT..V.QHK...IALKK..
Retrocopy VFNHLGSDRACRFCKLLELSK-DDVHQHAVRKPLNKEGKKPRTQTLKIQHLVTSQVFQHKCQHIALKKHC

Parental  TKKIKEEAAEYAKLLAKRMKAKKR-QEQIAQESRLSSLRASPSSESQ
          .K.....AAEYAKLL.KRM.AK...QEQ.......SSLRAS.S...Q
Retrocopy NKEV---AAEYAKLLTKRMEAKEKCQEQSVKKHGMSSLRASTSKSVQ

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_33 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 16 parental genes, and 113 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Canis familiaris	ENSCAFG00000001615	4 retrocopies	retro_cfam_184, retro_cfam_1936, retro_cfam_48, retro_cfam_87,
Callithrix jacchus	ENSCJAG00000020612	6 retrocopies	retro_cjac_1246, retro_cjac_18, retro_cjac_180, retro_cjac_190, retro_cjac_2982, retro_cjac_59,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Dasypus novemcinctus	ENSDNOG00000007241	1 retrocopy	retro_dnov_1192,
Ficedula albicollis	ENSFALG00000003078	1 retrocopy	retro_falb_24,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Macaca mulatta	ENSMMUG00000003412	1 retrocopy	retro_mmul_263,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Mus musculus	ENSMUSG00000028495	45 retrocopies	retro_mmus_1010, retro_mmus_1126, retro_mmus_1291, retro_mmus_1357, retro_mmus_1436, retro_mmus_1590, retro_mmus_1663, retro_mmus_1701, retro_mmus_1720, retro_mmus_1966, retro_mmus_1969, retro_mmus_2047, retro_mmus_2068, retro_mmus_2146, retro_mmus_2167, retro_mmus_2171, retro_mmus_2336, retro_mmus_2342, retro_mmus_2367, retro_mmus_2369, retro_mmus_2489, retro_mmus_2546, retro_mmus_2593, retro_mmus_2601, retro_mmus_2625, retro_mmus_2824, retro_mmus_2845, retro_mmus_2946, retro_mmus_3154, retro_mmus_324, retro_mmus_3256, retro_mmus_3338, retro_mmus_3498, retro_mmus_3633, retro_mmus_475, retro_mmus_477, retro_mmus_478, retro_mmus_568, retro_mmus_588, retro_mmus_617, retro_mmus_716, retro_mmus_743, retro_mmus_748, retro_mmus_895, retro_mmus_938,
Ochotona princeps	ENSOPRG00000000751	6 retrocopies	retro_opri_1111, retro_opri_1187, retro_opri_248, retro_opri_33 , retro_opri_466, retro_opri_865,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Pongo abelii	ENSPPYG00000019193	15 retrocopies	retro_pabe_1024, retro_pabe_1625, retro_pabe_2065, retro_pabe_2616, retro_pabe_2617, retro_pabe_2882, retro_pabe_2964, retro_pabe_3282, retro_pabe_3481, retro_pabe_3777, retro_pabe_629, retro_pabe_730, retro_pabe_822, retro_pabe_850, retro_pabe_955,
Rattus norvegicus	ENSRNOG00000049025	8 retrocopies	retro_rnor_1008, retro_rnor_1189, retro_rnor_1988, retro_rnor_1990, retro_rnor_2085, retro_rnor_2635, retro_rnor_479, retro_rnor_718,
Sarcophilus harrisii	ENSSHAG00000005486	1 retrocopy	retro_shar_549,
Vicugna pacos	ENSVPAG00000006030	10 retrocopies	retro_vpac_217, retro_vpac_228, retro_vpac_288, retro_vpac_297, retro_vpac_392, retro_vpac_407, retro_vpac_412, retro_vpac_438, retro_vpac_618, retro_vpac_70,