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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattcccaattaatttgctactgcctgcttccactgctgcagtgcttatgatatatcatgcctactgtagtatatatgtaatgtaatacaaggattaagtatgtccttcctgaatgatgatggatgattgctgagtttctccttccttggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCTTTGCTAG

Basic information

species Oryza sativa
transcript LOC_Os01g73910.6
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|428435|gb|D24584.1|D24584
EST:     CCGNCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|58590372|gb|CF988680.1|CF988680
EST:     CGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGAGGGAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGCGCTTAATGATATGGGCAAGGC
genomic: CGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGA-CAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGC
EST: gi|88688286|gb|CI731862.1|CI731862
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|2427812|gb|C72275.1|C72275
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|88411775|gb|CI571267.1|CI571267
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|33380975|gb|CF196318.1|CF196318
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGC
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGC
EST: gi|88664563|gb|CI699578.1|CI699578
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|13806000|gb|AU181304.1|AU181304
EST:     CCGCCCGGGGCCTTGATGGAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|88762070|gb|CI771626.1|CI771626
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|58591227|gb|CF989535.1|CF989535
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AAGACACTGCTGCTGAGAGCAGTTCCACGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|88312036|gb|CI580201.1|CI580201
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGGT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|29683738|gb|CB680013.1|CB680013
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAACAG                         AACACACTGCTGCTGAGAGCAATTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|88454163|gb|CI694086.1|CI694086
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|13806135|gb|AU181375.1|AU181375
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|88689580|gb|CI733156.1|CI733156
EST:     CCGCCCGGGGCCTTGATGCAGAAGACTTCCGCCATCCGCTGGACAAGCAC                         AACACACTGNTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
EST: gi|29624825|gb|CB629836.1|CB629836
EST:     CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAG                         AACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT
genomic: CCGCCCGGGGCCTTGATGCAGACGACTTCCGCCATCCGCTGGACAAGCAGgtgaattccc ... tggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccttcctgaatgatgatggatgattgctgagtttctccttccttggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCTTTGCTAG
                                 tttctccttccttggc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattcccaattaatttgctactgcctgcttccactgctgcagtgcttatgatatatcatgcctactgtagtatatatgtaatgtaatacaaggattaagtatgtccttcctgaatgatgatggatgattgctgagtttctccttccttggcctgcagAACACACTGCTGCTGAGAGCAGTTCCAGGGCTTAATGATATGGGCAAGGCTTTGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG