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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatgtattgtggacttccattaattgtcgtcacttggcatatgcagaactcatcgccccagtttgcattgtttctaagccattgtttttctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAACATATGACACAAACTGCTGAACGTGCCAATCAGTCCCTGTCGCTCGTGTG

Basic information

species Oryza sativa
transcript LOC_Os01g17250.1
intron # 5
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|88507676|gb|CI435182.1|CI435182
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|87025893|gb|CI282470.1|CI282470
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|15849919|gb|BI798195.1|BI798195
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACCAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAA
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGAC-AAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAA
EST: gi|86828695|gb|CI280551.1|CI280551
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|88221261|gb|CI221217.1|CI221217
EST:     TGCGGCACGATTCTTACTAGCGGGCCTTTTGAGCATATACCCCTGAACGA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|29668540|gb|CB664815.1|CB664815
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|86530237|gb|CI170443.1|CI170443
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|86506444|gb|CI149077.1|CI149077
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|86533916|gb|CI174122.1|CI174122
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTNNNNNNNCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|88226240|gb|CI226156.1|CI226156
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|88515049|gb|CI442703.1|CI442703
EST:     TNCGGCACGATTCCTANTAGCGGGCCTTTTGAGCATATACCCCTGGACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|86420332|gb|CI056321.1|CI056321
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|58686473|gb|CK075160.1|CK075160
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|7206590|gb|C97644.2|C97644
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
EST: gi|88838832|gb|CI012708.1|CI012708
EST:     TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAA                         CTTTGACCAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC
genomic: TGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAAC

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: 69 (upstream exon), 75 (downstream exon)
Score: 25

AGATGTCTCGAACAATGATCTTTGCGGCACGATTCCTACTAGCGGGCCTTTTGAGCATATACCCCTGAACAAgtaagatcta ... ctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAACATATGACACAAACTGCTGAACGTGCCAATCAGTCCCTGTCGCTCGTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaactcatcgccccagtttgcattgtttctaagccattgtttttctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAACATATGACACAAACTGCTGAACGTGCCAATCAGTCCCTGTCGCTCGTGTG
                                  ccattgtttttctctc  CT-rich tract
                                    attgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatgtattgtggacttccattaattgtcgtcacttggcatatgcagaactcatcgccccagtttgcattgtttctaagccattgtttttctctctgcagCTTTGACAAAAATCCAAGGTTGGAGGGGCCCGAGTTGCAAGGGCTTGCAACATATGACACAAACTGCTGAACGTGCCAATCAGTCCCTGTCGCTCGTGTG

-tatgtat
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