RetrogeneDB ID: retro_opri_1172

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_87:152400..152717(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXN
• Ensembl ID: ENSOPRG00000013805
• Aliases: None
• Description: thioredoxin [Source:HGNC Symbol;Acc:12435]

Sequence

>retro_opri_1172
ATGGTGAAGCAGATCACAAGCAAGTCTGCTTTTCAGGAAGTGTTGGACTCTGCAGGAGATAAGCTAGTTGTGGTTGATTT
TCTCAGTCACATGGTGCGGACCCTGCAAGATGATCAAGCCATTCTTTCATTCCCTCTCTGAAAAATATTCCAACGTGCTG
TTTATTGAAGTAGGTGTGGACGACTGCCAGGATATCGCTGCAGACTGTGAAGTCAAGTGCATGCCAACCTTCCAGTTTTT
TTAAGAAGGGCCAGAAGGTGGGTGAATTTTCTGGAGCAAATAAGGAAAAACTTGAAGCCACCATTAATGAACGACTC

Alignment

ORF - retro_opri_1172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVKQIESKSAFQEVLDSAGDKLVVVDF-SATWCGPCKMIKPFFHSLSEKYSNVLFIEVDVDDCQDIAADC
          MVKQI.SKSAFQEVLDSAGDKLVVVDF.S.TWCGPCKMIKPFFHSLSEKYSNVLFIEV.VDDCQDIAADC
Retrocopy MVKQITSKSAFQEVLDSAGDKLVVVDF>SVTWCGPCKMIKPFFHSLSEKYSNVLFIEVGVDDCQDIAADC

Parental  EVKCMPTFQ-FFKKGQKVGEFSGANKEKLEATINELL
          EVKCMPTFQ.FFKKGQKVGEFSGANKEKLEATINE.L
Retrocopy EVKCMPTFQ>FFKKGQKVGEFSGANKEKLEATINERL

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_1172 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 22 parental genes, and 119 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013018	3 retrocopies	retro_acar_112, retro_acar_121, retro_acar_122,
Choloepus hoffmanni	ENSCHOG00000011506	10 retrocopies	retro_chof_1111, retro_chof_127, retro_chof_1557, retro_chof_1680, retro_chof_1696, retro_chof_240, retro_chof_2424, retro_chof_317, retro_chof_617, retro_chof_82,
Callithrix jacchus	ENSCJAG00000017321	5 retrocopies	retro_cjac_1407, retro_cjac_2536, retro_cjac_2733, retro_cjac_3010, retro_cjac_69,
Cavia porcellus	ENSCPOG00000015348	5 retrocopies	retro_cpor_1048, retro_cpor_49, retro_cpor_54, retro_cpor_55, retro_cpor_74,
Dasypus novemcinctus	ENSDNOG00000019205	20 retrocopies	retro_dnov_100, retro_dnov_1047, retro_dnov_1122, retro_dnov_1222, retro_dnov_1353, retro_dnov_1403, retro_dnov_1404, retro_dnov_1628, retro_dnov_1634, retro_dnov_1646, retro_dnov_1949, retro_dnov_1996, retro_dnov_2069, retro_dnov_2197, retro_dnov_2239, retro_dnov_290, retro_dnov_466, retro_dnov_593, retro_dnov_843, retro_dnov_852,
Echinops telfairi	ENSETEG00000003065	13 retrocopies	retro_etel_1173, retro_etel_1256, retro_etel_1672, retro_etel_1725, retro_etel_1807, retro_etel_1831, retro_etel_1932, retro_etel_1956, retro_etel_320, retro_etel_389, retro_etel_737, retro_etel_903, retro_etel_926,
Homo sapiens	ENSG00000136810	7 retrocopies	retro_hsap_1713, retro_hsap_206, retro_hsap_2330, retro_hsap_3052, retro_hsap_3614, retro_hsap_405, retro_hsap_736,
Gorilla gorilla	ENSGGOG00000006925	6 retrocopies	retro_ggor_1283, retro_ggor_1769, retro_ggor_2440, retro_ggor_35, retro_ggor_401, retro_ggor_620,
Loxodonta africana	ENSLAFG00000012856	2 retrocopies	retro_lafr_372, retro_lafr_93,
Macropus eugenii	ENSMEUG00000003515	8 retrocopies	retro_meug_1198, retro_meug_1204, retro_meug_1603, retro_meug_192, retro_meug_2170, retro_meug_2175, retro_meug_539, retro_meug_840,
Microcebus murinus	ENSMICG00000002128	2 retrocopies	retro_mmur_118, retro_mmur_717,
Macaca mulatta	ENSMMUG00000010322	1 retrocopy	retro_mmul_167,
Mus musculus	ENSMUSG00000028367	2 retrocopies	retro_mmus_3063, retro_mmus_432,
Otolemur garnettii	ENSOGAG00000009165	6 retrocopies	retro_ogar_1573, retro_ogar_2763, retro_ogar_3141, retro_ogar_3205, retro_ogar_727, retro_ogar_851,
Ochotona princeps	ENSOPRG00000013805	11 retrocopies	retro_opri_1132, retro_opri_1172 , retro_opri_220, retro_opri_309, retro_opri_468, retro_opri_643, retro_opri_681, retro_opri_738, retro_opri_81, retro_opri_887, retro_opri_89,
Procavia capensis	ENSPCAG00000014011	1 retrocopy	retro_pcap_311,
Pongo abelii	ENSPPYG00000019491	2 retrocopies	retro_pabe_1428, retro_pabe_2965,
Pan troglodytes	ENSPTRG00000021245	7 retrocopies	retro_ptro_1158, retro_ptro_1703, retro_ptro_1988, retro_ptro_2444, retro_ptro_309, retro_ptro_339, retro_ptro_524,
Rattus norvegicus	ENSRNOG00000012081	1 retrocopy	retro_rnor_616,
Sarcophilus harrisii	ENSSHAG00000006739	1 retrocopy	retro_shar_329,
Ictidomys tridecemlineatus	ENSSTOG00000020668	4 retrocopies	retro_itri_6, retro_itri_714, retro_itri_823, retro_itri_884,
Tupaia belangeri	ENSTBEG00000011193	2 retrocopies	retro_tbel_1293, retro_tbel_3405,