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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttatccaactatatgcatcgaaacttatttgtctagaacttcaattgaattgcttgcttgcttgttaacatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG

Basic information

species Oryza sativa
transcript LOC_Os03g62640.2
intron # 3
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|29623140|gb|CB628151.1|CB628151
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29623911|gb|CB628922.1|CB628922
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29661287|gb|CB657562.1|CB657562
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29630312|gb|CB635321.1|CB635321
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29624088|gb|CB629099.1|CB629099
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAC                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29681987|gb|CB678262.1|CB678262
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAC                         ACAGATGAGGTGTTGCACTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29672226|gb|CB668501.1|CB668501
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29679242|gb|CB675517.1|CB675517
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|88689613|gb|CI733189.1|CI733189
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29627005|gb|CB632016.1|CB632016
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29635022|gb|CB640031.1|CB640031
EST:     ATGAGGATGCCAAAGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAA                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29681845|gb|CB678120.1|CB678120
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29681724|gb|CB677999.1|CB677999
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29678406|gb|CB674681.1|CB674681
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29629756|gb|CB634765.1|CB634765
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29680593|gb|CB676868.1|CB676868
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29674493|gb|CB670768.1|CB670768
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAC                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCTAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29664072|gb|CB660347.1|CB660347
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29660244|gb|CB656519.1|CB656519
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29636080|gb|CB641089.1|CB641089
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAN                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29639321|gb|CB644330.1|CB644330
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29629579|gb|CB634588.1|CB634588
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29617712|gb|CB622724.1|CB622724
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29665628|gb|CB661903.1|CB661903
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGGTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29629757|gb|CB634766.1|CB634766
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29674744|gb|CB671019.1|CB671019
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCT--GCTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29678347|gb|CB674622.1|CB674622
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29626366|gb|CB631377.1|CB631377
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|88367212|gb|CI563976.1|CI563976
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGGAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA
EST: gi|29656040|gb|CB652315.1|CB652315
EST:     ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAG                         ACAGATGAGGTGTTGCAGTTGTCAAGGGAGATCGAGGAAAAAATGAAAGAA
genomic: ATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAA

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: 44 (upstream exon), 56 (downstream exon)
Score: 18

CATCGTGGAGTGCGAGAGGAAAATTCAGAGGGCGCTGAAGCGTCTTGCTGATGAGGATGCCAAGGCTGCTATTGCAATATCTGTTTCTGAGGTTACTCAGgtatttatcc ... acatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttatttgtctagaacttcaattgaattgcttgcttgcttgttaacatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG
                                        tgttaac  putative branch site (score: 18)
                    aattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttatccaactatatgcatcgaaacttatttgtctagaacttcaattgaattgcttgcttgcttgttaacatttgcagACAGATGAGGTGTTGCAGTTGTCAAAGGAGATCAAGGAAAAAATGAAAGAAGTTGATACCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT