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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgaagtttattttttatgtttcagcgagcttccttcagaacaatcatgattattcatgtgtggcctgaaacttttcttcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTTACTTGGAAGAGGTGGTTTGCCTTGAGTAGATCAAAACCTACATTTGGGG

Basic information

species Oryza sativa
transcript LOC_Os06g47890.2
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29617828|gb|CB622840.1|CB622840
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|88969987|gb|CI383489.1|CI383489
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|89196059|gb|CI395477.1|CI395477
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|88480244|gb|CI417515.1|CI417515
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCCACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|58685461|gb|CK074148.1|CK074148
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|29664504|gb|CB660779.1|CB660779
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCCCAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|58692053|gb|CK080740.1|CK080740
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|29677426|gb|CB673701.1|CB673701
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|58691409|gb|CK080096.1|CK080096
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|88851303|gb|CI404355.1|CI404355
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|29637547|gb|CB642556.1|CB642556
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|88513232|gb|CI440738.1|CI440738
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|29629693|gb|CB634702.1|CB634702
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
EST: gi|4715036|gb|AU056153.1|AU056153
EST:     GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAG                         GACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT
genomic: GATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 73 (downstream exon)
Score: 29

GTTGGAGGAACAAAAGCAATAGTGCTTGGAGGACAAACTGGAGAAGAGTGGATGTTAACCGAAATCCATGAGCTTTCTTTGGCTAGCAGCACAGTTTGAGgttcgaagtt ... tcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTTACTTGGAAGAGGTGGTTTGCCTTGAGTAGATCAAAACCTACATTTGGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagaacaatcatgattattcatgtgtggcctgaaacttttcttcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTTACTTGGAAGAGGTGGTTTGCCTTGAGTAGATCAAAACCTACATTTGGGG
                                      cttttcttcact  CT-rich tract
             atgattatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgaagtttattttttatgtttcagcgagcttccttcagaacaatcatgattattcatgtgtggcctgaaacttttcttcactggcagGACTGGAACACTGGATGAGTATACTGAATCTTTTGGCAACGACTTGTATTTACTTGGAAGAGGTGGTTTGCCTTGAGTAGATCAAAACCTACATTTGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA