RetrogeneDB ID: retro_opri_871

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_3930:89440..89860(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS27A
• Ensembl ID: ENSOPRG00000010469
• Aliases: None
• Description: ribosomal protein S27a [Source:HGNC Symbol;Acc:10417]

Sequence

>retro_opri_871
CTTACAGGGAAGACTACCACACTTGAGGTTGACCTGTTGGATACAACAAAAAATGTAAGACCCAATATCCAGGAAAAGGA
ACGTATTCTTTCTGATCTGCAAAGACTGATCTTCGCTGGCAAGCCACTGGAGTACGGACAGACTTCATCTGACTACAACA
TTCAAAAGGAGTGTATTCATGTGTTGGGACTTTGTGGTGGTGGTAAGAAAAGCAAGTCTTACACCACTCCTAAGAGGAAT
AAGCACAAGACAAAGATTAAGTCAGGTGTCCTGAAGTACAAGAATGGGAGATTTAGCTGCTTATGTAGCAGTACCCTTCA
GGTGAATGTGGTGTTGGGAGTGTTCACATCAGCCATTCTGACAGACATTACCGTGGGTGAATGCTGTTTGACTTACTGCT
TCCACAAACCAGAAAGCAAG

Alignment

ORF - retro_opri_871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.93 %
• Parental protein coverage: 96.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGA
          LTGKT.TLEV...DT..NV...IQ.KE.I..D.QRLIFAGK.LE.G.T.SDYNIQKE...H.VL.L.GG.
Retrocopy LTGKTTTLEVDLLDTTKNVRPNIQEKERILSDLQRLIFAGKPLEYGQTSSDYNIQKE-CIH-VLGLCGGG

Parental  KKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKIS-RLRRECPSDECGAGVFMASHFDRHY-CGKCC
          K..K.KSYTTPK.NKHK..K.K..VLKY.....NG..S..L....PS.ECG.G....SH.DRHY..G.CC
Retrocopy K--KSKSYTTPKRNKHK-TKIKSGVLKY----KNGRFS<LLM*QYPSGECGVGSVHISHSDRHY>VGECC

Parental  LTYCFNKPEDK
          LTYCF.KPE.K
Retrocopy LTYCFHKPESK

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_871 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 15 parental genes, and 78 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004017	5 retrocopies	retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Canis familiaris	ENSCAFG00000023471	3 retrocopies	retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus	ENSCJAG00000010052	5 retrocopies	retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Gorilla gorilla	ENSGGOG00000007678	9 retrocopies	retro_ggor_1290, retro_ggor_1291, retro_ggor_1502, retro_ggor_1749, retro_ggor_179, retro_ggor_203, retro_ggor_2373, retro_ggor_2858, retro_ggor_2885,
Loxodonta africana	ENSLAFG00000023133	2 retrocopies	retro_lafr_1122, retro_lafr_185,
Myotis lucifugus	ENSMLUG00000017064	10 retrocopies	retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus	ENSMLUG00000029449	1 retrocopy	retro_mluc_1585,
Macaca mulatta	ENSMMUG00000015563	8 retrocopies	retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica	ENSMODG00000001819	3 retrocopies	retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Oryctolagus cuniculus	ENSOCUG00000003613	10 retrocopies	retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Ochotona princeps	ENSOPRG00000010469	13 retrocopies	retro_opri_1056, retro_opri_1120, retro_opri_162, retro_opri_177, retro_opri_191, retro_opri_331, retro_opri_472, retro_opri_490, retro_opri_582, retro_opri_71, retro_opri_717, retro_opri_801, retro_opri_871 ,
Pongo abelii	ENSPPYG00000025871	1 retrocopy	retro_pabe_117,
Pan troglodytes	ENSPTRG00000011928	1 retrocopy	retro_ptro_32,
Rattus norvegicus	ENSRNOG00000004426	2 retrocopies	retro_rnor_117, retro_rnor_161,
Ictidomys tridecemlineatus	ENSSTOG00000009566	5 retrocopies	retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,