RetrogeneDB ID:

retro_pabe_1428

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:17:4487792..4488153(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TXN
Ensembl ID:ENSPPYG00000019491
Aliases:None
Description:thioredoxin [Source:RefSeq peptide;Acc:NP_001125903]


Retrocopy-Parental alignment summary:






>retro_pabe_1428
CCTATTAAAAAAAAAAAAAAAGCTGCTCATCAGACCTCAGCGGCCAAGATGGTGAAGCAGATCGAGAGCAAGCTTGCTTT
TTAGGAAGCCTTGGATGTCACAGGCGGTAAACGTGTAGTAGTTGACTTCTCAGCCACATGGTGTGGGCCTTGCAAATGAT
CAAGCCTTTCTTTATCCCCTCTCTGGAAAGTATTCCAACGTGGTATTCCTTGAAGTAGATGTGGATGACTGTCAGGATGT
TGCTTCAGAGTGTGAAGCCAAATGCATGCCAACATTCCAGTTTTTTAAGAAGGGACAAAAGGTGGGTGAATTTTCTGGAG
CCCATAAGGAAAAGCTTGAAGCCACCATTCATGAATTAGTC

ORF - retro_pabe_1428 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.3 %
Parental protein coverage: 55.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalPFPSVLTAARQTPAAKMVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPCK-MIKPFF-HSLSEKYSNV
P......AA.QT.AAKMVKQIESK.AF.EALD..G.K.VVVDFSATWCGPCK.MIKPFF...LS.KYSNV
RetrocopyPIXXXXXAAHQTSAAKMVKQIESKLAF*EALDVTGGKRVVVDFSATWCGPCK<MIKPFF<YPLSGKYSNV
ParentalIFLEVDVDDCQDVASECEVKCMPTFQFFKKGQKVGEFSGANKEKLEATINELV
.FLEVDVDDCQDVASECE.KCMPTFQFFKKGQKVGEFSGA.KEKLEATI.ELV
RetrocopyVFLEVDVDDCQDVASECEAKCMPTFQFFKKGQKVGEFSGAHKEKLEATIHELV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .06 RPM 45 .12 RPM
SRP007412_cerebellum 0 .00 RPM 47 .30 RPM
SRP007412_heart 0 .00 RPM 21 .98 RPM
SRP007412_kidney 0 .10 RPM 76 .90 RPM
SRP007412_liver 0 .00 RPM 62 .67 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_1428 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1428 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1428 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1713
Pan troglodytes retro_ptro_1158
Gorilla gorilla retro_ggor_1283
Parental genes homology:
Parental genes homology involve 32 parental genes, and 140 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000130183 retrocopies
retro_acar_112, retro_acar_121, retro_acar_122,
Ailuropoda melanoleuca ENSAMEG000000180173 retrocopies
retro_amel_1559, retro_amel_211, retro_amel_217,
Bos taurus ENSBTAG000000029532 retrocopies
retro_btau_1267, retro_btau_418,
Choloepus hoffmanni ENSCHOG0000001150610 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 ENSCJAG000000173215 retrocopies
retro_cjac_1407, retro_cjac_2536, retro_cjac_2733, retro_cjac_3010, retro_cjac_69,
Cavia porcellus ENSCPOG000000153485 retrocopies
retro_cpor_1048, retro_cpor_49, retro_cpor_54, retro_cpor_55, retro_cpor_74,
Dasypus novemcinctus ENSDNOG0000001920520 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,
Equus caballus ENSECAG000000133241 retrocopy
retro_ecab_51,
Echinops telfairi ENSETEG0000000306513 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,
Felis catus ENSFCAG000000047904 retrocopies
retro_fcat_1096, retro_fcat_1105, retro_fcat_2025, retro_fcat_877,
Homo sapiens ENSG000001368107 retrocopies
retro_hsap_1713, retro_hsap_206, retro_hsap_2330, retro_hsap_3052, retro_hsap_3614, retro_hsap_405, retro_hsap_736,
Gorilla gorilla ENSGGOG000000069256 retrocopies
retro_ggor_1283, retro_ggor_1769, retro_ggor_2440, retro_ggor_35, retro_ggor_401, retro_ggor_620,
Loxodonta africana ENSLAFG000000128562 retrocopies
retro_lafr_372, retro_lafr_93,
Macropus eugenii ENSMEUG000000035158 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 ENSMICG000000021282 retrocopies
retro_mmur_118, retro_mmur_717,
Myotis lucifugus ENSMLUG000000090653 retrocopies
retro_mluc_1268, retro_mluc_1940, retro_mluc_776,
Macaca mulatta ENSMMUG000000103221 retrocopy
retro_mmul_167,
Mustela putorius furoENSMPUG000000074263 retrocopies
retro_mputfur_1230, retro_mputfur_693, retro_mputfur_840,
Mus musculus ENSMUSG000000283672 retrocopies
retro_mmus_3063, retro_mmus_432,
Otolemur garnettii ENSOGAG000000091656 retrocopies
retro_ogar_1573, retro_ogar_2763, retro_ogar_3141, retro_ogar_3205, retro_ogar_727, retro_ogar_851,
Ochotona princeps ENSOPRG0000001380511 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 ENSPCAG000000140111 retrocopy
retro_pcap_311,
Pongo abelii ENSPPYG00000019491 2 retrocopies
retro_pabe_1428 , retro_pabe_2965,
Pan troglodytes ENSPTRG000000212457 retrocopies
retro_ptro_1158, retro_ptro_1703, retro_ptro_1988, retro_ptro_2444, retro_ptro_309, retro_ptro_339, retro_ptro_524,
Pteropus vampyrus ENSPVAG000000072651 retrocopy
retro_pvam_433,
Rattus norvegicus ENSRNOG000000120811 retrocopy
retro_rnor_616,
Sorex araneus ENSSARG000000074652 retrocopies
retro_sara_373, retro_sara_525,
Sarcophilus harrisii ENSSHAG000000067391 retrocopy
retro_shar_329,
Sus scrofa ENSSSCG000000054531 retrocopy
retro_sscr_786,
Ictidomys tridecemlineatus ENSSTOG000000206684 retrocopies
retro_itri_6, retro_itri_714, retro_itri_823, retro_itri_884,
Tupaia belangeri ENSTBEG000000111932 retrocopies
retro_tbel_1293, retro_tbel_3405,
Tursiops truncatus ENSTTRG000000001191 retrocopy
retro_ttru_1378,


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