Basic Information
Gene Model:Bol027262
Gene Family:Not classificated
Chromosome:C04
Scaffold:Scaffold000077
Sequence:
 | 
Gene Structure
Nucleotide Length:5663 bp
Transcript Length:1797 bp
Protein Length:598 aa
Strand:-
Location:C04: 20160334 : 20165996
Gene CDSs(19): 1-172 | 252-435 | 1595-1665 | 1785-1836 | 1939-2023 | 2119-2196 | 2293-2409 | 2550-2654 | 2741-2815 | 3106-3165 | 3240-3335 | 3626-3742 | 4056-4177 | 4269-4410 | 4542-4628 | 4931-4993 | 5076-5147 | 5465-5550 | 5651-5663 |
Protein Sequence Features
Interpro
DatabaseTermsIdentifierStartEndE-valueInterPro IDDescription
HMMSmartSM00320no description 425 460 36IPR001680WD40 repeat
HMMSmartSM00320no description 384 422 1.3e-08IPR001680WD40 repeat
HMMSmartSM00320no description 340 381 0.68IPR001680WD40 repeat
HMMSmartSM00320no description 298 337 1.9e-05IPR001680WD40 repeat
HMMSmartSM00320no description 208 250 2.6IPR001680WD40 repeat
HMMSmartSM00320no description 253 292 1.6e-09IPR001680WD40 repeat
HMMSmartSM00504no description 1 66 8.6e-20IPR003613U box domain
Coilcoilcoiled-coil 115 136 NANot foundNot found
superfamilySSF57850RING/U-box 1 53 3.1e-14Not foundNot found
superfamilySSF50978WD40 repeat-like 154 500 1.2e-53IPR011046WD40 repeat-like-containing domain
Gene3DG3DSA:3.30.40.10no description 1 56 1.2e-18Not foundNot found
Gene3DG3DSA:2.130.10.10no description 176 500 4.8e-49IPR015943WD40/YVTN repeat-like-containing domain
ProfileScanPS50845RETICULON 481 598 14.536IPR003388Reticulon
ProfileScanPS50294WD_REPEATS_REGION 218 431 35.383IPR017986WD40-repeat-containing domain
ProfileScanPS50082WD_REPEATS_2 357 390 9.807IPR019782WD40 repeat 2
ProfileScanPS50082WD_REPEATS_2 391 431 12.146IPR019782WD40 repeat 2
ProfileScanPS50082WD_REPEATS_2 305 346 9.172IPR019782WD40 repeat 2
ProfileScanPS50082WD_REPEATS_2 260 291 14.786IPR019782WD40 repeat 2
HMMPantherPTHR13889PRE-MRNA SPLICING FA 42 480 0Not foundNot found
HMMPantherPTHR13889:SF9PRE-MRNA SPLICING FA 42 480 0Not foundNot found
HMMPfamPF02453Reticulon 516 591 8.4e-07IPR003388Reticulon
HMMPfamPF02453Reticulon 481 496 0.00013IPR003388Reticulon
HMMPfamPF00400WD40 385 422 9.6e-11IPR019781WD40 repeat, subgroup
HMMPfamPF00400WD40 299 337 7.8e-08IPR019781WD40 repeat, subgroup
HMMPfamPF00400WD40 254 292 9.5e-15IPR019781WD40 repeat, subgroup
HMMPfamPF08606Prp19 64 133 2.7e-47IPR013915Pre-mRNA-splicing factor 19
Gene Ontology
GO TermGO TypeDescription
GO:0000151 Cellular Component ubiquitin ligase complex
GO:0004842 Molecular Function ubiquitin-protein ligase activity
GO:0005783 Cellular Component endoplasmic reticulum
GO:0016567 Biological Process protein ubiquitination
Swiss-Prot
Best HitE_value Description
O227850.0PR19B_ARATH Pre-mRNA-processing factor 19 homolog 2 OS=Arabidopsis thaliana GN=PUB60 PE=2 SV=2
TrEMBL
Best HitE_value Description
Q3EBP50.0Q3EBP5_ARATH Truncated MOS4-associated complex protein 3B OS=Arabidopsis thaliana GN=MAC3B PE=2 SV=2
KEGG
Best HitE_valueKOEC or Symbol Description
ath:AT2G333400.0K10599PRPF19, PRP19pre-mRNA-processing factor 19
Gene Cluster
Orthologs
OrthoMCL GroupSpeciesGene List
ORTHOMCL1431(17 genes,8 taxa):Arabidopsis thalianaAT1G04510.1
ORTHOMCL1431(17 genes,8 taxa):Arabidopsis thalianaAT2G33340.1
ORTHOMCL1431(17 genes,8 taxa):Brassica oleraceaBol011585
ORTHOMCL1431(17 genes,8 taxa):Brassica oleraceaBol027262
ORTHOMCL1431(17 genes,8 taxa):Brassica oleraceaBol037940
ORTHOMCL1431(17 genes,8 taxa):Brassica oleraceaBol040899
ORTHOMCL1431(17 genes,8 taxa):Brassica rapaBra005504
ORTHOMCL1431(17 genes,8 taxa):Brassica rapaBra015322
ORTHOMCL1431(17 genes,8 taxa):Brassica rapaBra021844
ORTHOMCL1431(17 genes,8 taxa):Brassica rapaBra030575
ORTHOMCL1431(17 genes,8 taxa):Vitis viniferaGSVIVT01027911001
ORTHOMCL1431(17 genes,8 taxa):Oryza sativaOs10t0466300-01
ORTHOMCL1431(17 genes,8 taxa):Oryza sativaOs10t0466300-02
ORTHOMCL1431(17 genes,8 taxa):Populus trichocarpaPOPTR_0008s17140.1
ORTHOMCL1431(17 genes,8 taxa):Populus trichocarpaPOPTR_0010s07660.1
ORTHOMCL1431(17 genes,8 taxa):Sorghum bicolorSb01g019790.1
ORTHOMCL1431(17 genes,8 taxa):Carica papayaevm.TU.supercontig_44.4
Tandem Duplication
ClusterGene Num.Gene List

The tandem genes of this gene was not detected with strict parameters, so there is no information collected in Bolbase.

Synteny Analysis
Synteny Genes
Compared to A.thaliana Compared to B.rapa
Synteny Regions
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC04:18992445..21825121 (+)A.thalianaChr2:13722427..14926591 (+)187
SpeciesRegionMapped SpeciesMapped RegionNum. of Genewise
B.oleraceaC04:19201735..21825121 (+)B.rapaA05:21833239..23208305 (-)183
Trplicated Block
BlockBest HitStartENDChromosomeSubgenomeNum. of Gene Pairs on Block
JAT2G333401412621714131143Chr2Subgenome_III(LF)205
 
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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