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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtataagatattatgcaacaattaccatctttgcctgcattcttcgtcctttagattgaagttatgtcatttgcctgataatttgattgttctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG

Basic information

species Oryza sativa
transcript LOC_Os03g20520.1
intron # 11
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|88221975|gb|CI221931.1|CI221931
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|86851807|gb|CI316376.1|CI316376
EST:     CCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|218482003|gb|FG956575.1|FG956575
EST:     CCAGGCCTCCGCCTGGNGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|88266278|gb|CI377180.1|CI377180
EST:     TTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: TTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|5002852|gb|AU067961.1|AU067961
EST:     TCTATGAATTTNCTCCCAATTAAG                         GTTGATTTTACTGAAGAAAATCCATCGCTTCTTCACTTCCTGACAAACAT
genomic: TCTATGAATTTTCT-CCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACAT
EST: gi|218492797|gb|FG953626.1|FG953626
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACAT
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTG-AAGAAAATACATCGCTTCTTCACTTCCTGACAAACAT
EST: gi|218505492|gb|FG958279.1|FG958279
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|25803052|gb|CA759013.1|CA759013
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|88847669|gb|CI018360.1|CI018360
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCCATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|88989740|gb|CI107427.1|CI107427
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|88256781|gb|CI359169.1|CI359169
EST:     CCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|89193410|gb|CI050708.1|CI050708
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACCAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|8859147|gb|AU096465.1|AU096465
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|701663|gb|D47954.1|D47954
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|89181360|gb|CI112866.1|CI112866
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|89189327|gb|CI048866.1|CI048866
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCCATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACCAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|58675353|gb|CK064040.1|CK064040
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|86873742|gb|CI341175.1|CI341175
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|86490016|gb|CI132649.1|CI132649
EST:     CTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|86429502|gb|CI076183.1|CI076183
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|29657637|gb|CB653912.1|CB653912
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|58690521|gb|CK079208.1|CK079208
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACGAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA
EST: gi|88844531|gb|CI020378.1|CI020378
EST:     CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCCATTAAG                         GTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACCAACATA
genomic: CCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATA

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: 26

TTTTCTGTGACGGAGCACTTTAGAGAAGCAATTGGCTATCCCAGGCCTCCGCCTGGTGTATATTTCTTCTATGAATTTTCTCCAATTAAGgtgaagaatg ... tctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcctttagattgaagttatgtcatttgcctgataatttgattgttctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG
                                         ttgttcttt  CT-rich tract
                                ataatttgattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataagatattatgcaacaattaccatctttgcctgcattcttcgtcctttagattgaagttatgtcatttgcctgataatttgattgttctttggcagGTTGATTTTACTGAAGAAAATACATCGCTTCTTCACTTCCTGACAAACATATGTGCTATTGTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - ttatgca
- - - - - - - - - - - - - - - ttgcctg
- - - - - - - - - - - - - - - -tgcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgt