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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatcgaagggatgagcttgtgctgttaatttttaatttccagtcaaaaacgaattgcttgttttctggtgctgtaacagtcaaaaccaaaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTATCCAAAGCTACTGATGATAGTCAAAGGTTATATGCAACTTCTTCTTGTG

Basic information

species Oryza sativa
transcript LOC_Os02g15870.1
intron # 2
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|58688297|gb|CK076984.1|CK076984
EST:     TG-CGCTGCG-TGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|33675137|gb|CF303376.1|CF303376
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|88573280|gb|CI664851.1|CI664851
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|33675745|gb|CF303984.1|CF303984
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|88742626|gb|CI766134.1|CI766134
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTG
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTG
EST: gi|29675363|gb|CB671638.1|CB671638
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|88424077|gb|CI689779.1|CI689779
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|29631823|gb|CB636832.1|CB636832
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|88736013|gb|CI759521.1|CI759521
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|88765983|gb|CI775073.1|CI775073
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTT
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTT
EST: gi|88403375|gb|CI573098.1|CI573098
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|88740170|gb|CI763678.1|CI763678
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCG
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCG
EST: gi|88336165|gb|CI647359.1|CI647359
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|88288481|gb|CI661686.1|CI661686
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|88762354|gb|CI771910.1|CI771910
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|33654216|gb|CF276830.1|CF276830
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|29631793|gb|CB636802.1|CB636802
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTA
EST: gi|88732838|gb|CI756015.1|CI756015
EST:     TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCG                         GTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAG
genomic: TGCCGCTGCGTTGCCTCTCCGAGCTGGCCCGCCGCCGGCCTGATCGCGCGgtgagattct ... aaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaaacgaattgcttgttttctggtgctgtaacagtcaaaaccaaaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTATCCAAAGCTACTGATGATAGTCAAAGGTTATATGCAACTTCTTCTTGTG
                           ctgtaac  putative branch site (score: 3)
                                                ttttc  putative PPT
                                      aaaaccaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacatcgaagggatgagcttgtgctgttaatttttaatttccagtcaaaaacgaattgcttgttttctggtgctgtaacagtcaaaaccaaaattttcagGTTGATGCAATGAGAGTGGGGCTCCGATGTTTGATGAGCACTTGCCCGTTATCCAAAGCTACTGATGATAGTCAAAGGTTATATGCAACTTCTTCTTGTG

- - - - - - - gagcttg
- - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - aaacgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaacc