RetrogeneDB ID: retro_opri_290

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4724:68530..68755(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPG
• Ensembl ID: ENSOPRG00000001093
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide G [Source:HGNC Symbol;Acc:11163]

Sequence

>retro_opri_290
ATGAGCAAAGCTCACCCTCCTGAGTTGAAAAAAATTATGGACAAGAAGTTGTCATTAAAATTAAATGACAGCAGACATGC
TCACGGAATACTGAGAGGATTTGATCCCTTCATGAATCTGGAGATAGGTGAATGTACGGAGATGGCAAATAGTGGACAGC
AGAACAATACTGGAACGGTGGTAATACGAGGAAACAGTATCATCATGTTAGAAGCCTTACAGCGA

Alignment

ORF - retro_opri_290 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMANSGQQNNIGMVVIRGNSIIML
          MSKAHPPELKK.MDKKLSLKLN..RH..GILRGFDPFMNL.I.EC.EMANSGQQNN.G.VVIRGNSIIML
Retrocopy MSKAHPPELKKIMDKKLSLKLNDSRHAHGILRGFDPFMNLEIGECTEMANSGQQNNTGTVVIRGNSIIML

Parental  EALER
          EAL.R
Retrocopy EALQR

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_290 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 19 parental genes, and 173 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016000	9 retrocopies	retro_amel_1577, retro_amel_1618, retro_amel_1671, retro_amel_1795, retro_amel_186, retro_amel_466, retro_amel_563, retro_amel_747, retro_amel_944,
Callithrix jacchus	ENSCJAG00000019313	18 retrocopies	retro_cjac_1034, retro_cjac_1227, retro_cjac_1398, retro_cjac_149, retro_cjac_1897, retro_cjac_223, retro_cjac_2419, retro_cjac_2431, retro_cjac_2658, retro_cjac_2795, retro_cjac_3246, retro_cjac_3314, retro_cjac_4078, retro_cjac_547, retro_cjac_763, retro_cjac_796, retro_cjac_897, retro_cjac_998,
Dipodomys ordii	ENSDORG00000005623	2 retrocopies	retro_dord_253, retro_dord_483,
Felis catus	ENSFCAG00000008118	8 retrocopies	retro_fcat_1006, retro_fcat_1092, retro_fcat_1248, retro_fcat_1467, retro_fcat_1893, retro_fcat_562, retro_fcat_82, retro_fcat_90,
Gorilla gorilla	ENSGGOG00000022169	3 retrocopies	retro_ggor_1413, retro_ggor_1672, retro_ggor_664,
Loxodonta africana	ENSLAFG00000002301	3 retrocopies	retro_lafr_428, retro_lafr_559, retro_lafr_887,
Microcebus murinus	ENSMICG00000015369	10 retrocopies	retro_mmur_1419, retro_mmur_1468, retro_mmur_1550, retro_mmur_265, retro_mmur_395, retro_mmur_59, retro_mmur_595, retro_mmur_625, retro_mmur_735, retro_mmur_901,
Myotis lucifugus	ENSMLUG00000026490	3 retrocopies	retro_mluc_273, retro_mluc_46, retro_mluc_731,
Macaca mulatta	ENSMMUG00000007961	3 retrocopies	retro_mmul_1021, retro_mmul_2048, retro_mmul_300,
Monodelphis domestica	ENSMODG00000011528	1 retrocopy	retro_mdom_1945,
Mustela putorius furo	ENSMPUG00000007221	2 retrocopies	retro_mputfur_100, retro_mputfur_114,
Nomascus leucogenys	ENSNLEG00000010182	1 retrocopy	retro_nleu_93,
Oryctolagus cuniculus	ENSOCUG00000011214	2 retrocopies	retro_ocun_1032, retro_ocun_57,
Ochotona princeps	ENSOPRG00000001093	6 retrocopies	retro_opri_290 , retro_opri_330, retro_opri_596, retro_opri_599, retro_opri_757, retro_opri_823,
Pongo abelii	ENSPPYG00000012324	14 retrocopies	retro_pabe_1054, retro_pabe_1078, retro_pabe_1079, retro_pabe_1169, retro_pabe_1188, retro_pabe_1465, retro_pabe_1603, retro_pabe_1728, retro_pabe_1929, retro_pabe_2041, retro_pabe_2160, retro_pabe_3093, retro_pabe_495, retro_pabe_95,
Rattus norvegicus	ENSRNOG00000016507	1 retrocopy	retro_rnor_409,
Ictidomys tridecemlineatus	ENSSTOG00000008654	11 retrocopies	retro_itri_1116, retro_itri_1260, retro_itri_128, retro_itri_1395, retro_itri_1871, retro_itri_280, retro_itri_353, retro_itri_572, retro_itri_589, retro_itri_910, retro_itri_947,
Tupaia belangeri	ENSTBEG00000017381	66 retrocopies	retro_tbel_1010, retro_tbel_1076, retro_tbel_1114, retro_tbel_1133, retro_tbel_1161, retro_tbel_1164, retro_tbel_1174, retro_tbel_121, retro_tbel_1288, retro_tbel_1448, retro_tbel_1461, retro_tbel_147, retro_tbel_1478, retro_tbel_149, retro_tbel_164, retro_tbel_1654, retro_tbel_1887, retro_tbel_1939, retro_tbel_1944, retro_tbel_1965, retro_tbel_1966, retro_tbel_1997, retro_tbel_2001, retro_tbel_2143, retro_tbel_217, retro_tbel_236, retro_tbel_239, retro_tbel_241, retro_tbel_2454, retro_tbel_2462, retro_tbel_2572, retro_tbel_2664, retro_tbel_2941, retro_tbel_3098, retro_tbel_3379, retro_tbel_3385, retro_tbel_343, retro_tbel_347, retro_tbel_3495, retro_tbel_3559, retro_tbel_3603, retro_tbel_362, retro_tbel_3699, retro_tbel_3980, retro_tbel_3981, retro_tbel_3983, retro_tbel_4010, retro_tbel_4011, retro_tbel_4177, retro_tbel_4196, retro_tbel_43, retro_tbel_4399, retro_tbel_4442, retro_tbel_4505, retro_tbel_4549, retro_tbel_4609, retro_tbel_465, retro_tbel_489, retro_tbel_697, retro_tbel_726, retro_tbel_736, retro_tbel_805, retro_tbel_921, retro_tbel_93, retro_tbel_936, retro_tbel_947,
Vicugna pacos	ENSVPAG00000007452	10 retrocopies	retro_vpac_182, retro_vpac_196, retro_vpac_25, retro_vpac_290, retro_vpac_295, retro_vpac_352, retro_vpac_42, retro_vpac_59, retro_vpac_591, retro_vpac_641,