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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGCACCGATTACTCCCAAGAAGATTGCACAGCCTGATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttcttctatctaataaaaatacaccgtgtttctattttttttgggttgtactgtgatgatgttttctgcctttatttcttgtgaagatgtttct...

Basic information

species Oryza sativa
transcript LOC_Os03g58480.1
intron # 3
splice site 5'
intron type U12 (go to U12 genes for details)

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|58684814|gb|CK073501.1|CK073501
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
EST: gi|218492089|gb|FG945536.1|FG945536
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
EST: gi|58597056|gb|CK007584.1|CK007584
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
EST: gi|58657562|gb|CK046242.1|CK046242
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
EST: gi|58665629|gb|CK054315.1|CK054315
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
EST: gi|33675922|gb|CF304161.1|CF304161
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAAC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAAC
EST: gi|218500899|gb|FG952816.1|FG952816
EST:     CTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: CTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
EST: gi|29628405|gb|CB633416.1|CB633416
EST:     ATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: ATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
EST: gi|58667605|gb|CK056291.1|CK056291
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
EST: gi|27554048|gb|CA997948.1|CA997948
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
EST: gi|33802668|gb|CF327205.1|CF327205
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGGCTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGGTGTTG
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGG-TGTTG
EST: gi|33676020|gb|CF304259.1|CF304259
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGC
EST: gi|33675598|gb|CF303837.1|CF303837
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAA
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAA
EST: gi|29628404|gb|CB633415.1|CB633415
EST:     GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTC                         AACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC
genomic: GATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGC

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: 73 (upstream exon), 75 (downstream exon)
Score: 73

ACTGCACCGATTACTCCCAAGAAGATTGCACAGCCTGATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttct ... ctgtgtaaagAACCACAACTTCAACAAGAGCTGGCAAAACCAAGGCAACTGTTGGTGTTGCCCCTTCATTTGTATGTGCTGATCGTGCTGACAAGAGAAAGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGCACCGATTACTCCCAAGAAGATTGCACAGCCTGATCATATGCTTCACCATCAAGAGGAGGACTCCTGCTCTGTGACTTCTTCgtatccttcttctatctaataaaaatacaccgtgtttctattttttttgggttgtactgtgatgatgttttctgcctttatttcttgtgaagatgtttct

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata