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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggctgcagctcaagctaattaaaaatatattttttttttcattctgatagcagctatattgatgcttgatctatggttcctattatgatatgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGCCCCTAAGCTCAACGAGAGGATCCTGTCCTCCTTGTCGAGGAGATCAGTA

Basic information

species Oryza sativa
transcript LOC_Os04g59040.1
intron # 1
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|87023771|gb|CI288124.1|CI288124
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|55433781|gb|CV730004.1|CV730004
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|3768324|gb|AU032351.1|AU032351
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|33794379|gb|CF323075.1|CF323075
EST:     CGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: CGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|88423146|gb|CI613447.1|CI613447
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|33681023|gb|CF309262.1|CF309262
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|88732604|gb|CI755781.1|CI755781
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|88300646|gb|CI587450.1|CI587450
EST:     AGCCGACACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: AGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|88427290|gb|CI586838.1|CI586838
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|88721865|gb|CI743377.1|CI743377
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|33686066|gb|CF314305.1|CF314305
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|58602895|gb|CK013423.1|CK013423
EST:     GCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAGGTCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCG
genomic: GCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCA-ATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCG
EST: gi|286879|gb|D15686.1|D15686
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGNCACTCCAATCCAAG                         GAGGATGAGTNAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|66915284|gb|CX102132.1|CX102132
EST:     TTCGCCGCCGCCGACACCTTCCACCCCTTCAGCCCCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|88726501|gb|CI750156.1|CI750156
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|27554006|gb|CA997906.1|CA997906
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|55433023|gb|CV729535.1|CV729535
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|86907275|gb|CI292840.1|CI292840
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|32948454|gb|BP185026.1|BP185026
EST:     CCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: CCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|58599062|gb|CK009590.1|CK009590
EST:     GCCGCCGCCACCTTCCACCCCTTCAGGCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: GCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|4878364|gb|AU062663.1|AU062663
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|55409712|gb|CV722088.1|CV722088
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|33693190|gb|CF321429.1|CF321429
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|58671895|gb|CK060581.1|CK060581
EST:     GCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: GCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|88742766|gb|CI766274.1|CI766274
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|163927162|gb|EG710251.1|EG710251
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|88405920|gb|CI591315.1|CI591315
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGGTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|25799147|gb|CA755108.1|CA755108
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|55434349|gb|CV730296.1|CV730296
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|163925905|gb|EG712281.1|EG712281
EST:     CCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: CCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
EST: gi|86848615|gb|CI293930.1|CI293930
EST:     TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAG                         GAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC
genomic: TTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGC

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), 74 (downstream exon)
Score: 67

GACGGAGGGTGCAGTGCAGTGCAGGGAATCATTTCATTTCTTCTTCTTCTTCGCCGCCGCCGCCACCTTCCACCCCTTCAGCCGCCACTCCAATCCAAGgtatcctctc ... atgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGCCCCTAAGCTCAACGAGAGGATCCTGTCCTCCTTGTCGAGGAGATCAGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagcagctatattgatgcttgatctatggttcctattatgatatgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGCCCCTAAGCTCAACGAGAGGATCCTGTCCTCCTTGTCGAGGAGATCAGTA
                                    tattatgatatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggctgcagctcaagctaattaaaaatatattttttttttcattctgatagcagctatattgatgcttgatctatggttcctattatgatatgatcatagGAGGATGAGTGAAGAGGACACCAATGCTGCTGCTGGGCAGCCCAGGCGCGCCCCTAAGCTCAACGAGAGGATCCTGTCCTCCTTGTCGAGGAGATCAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA