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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaagttgtcttgctaagattattttgttttacttctgatgtttatctgaagtggctccttttgggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACAAGTTGGTCCTAGTGGTTTATTTTTTACTGGGGATGGAACTGGTGAGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g45480.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45480.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G037200_T01 (Zea mays), 3'ss of exon 8
gtaagaaagttgtcttgctaagattattttg-----ttttacttctgatgt-ttatctgaagtggctccttttgggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACAAGTTGGTCCTAGTGGTTTATTTTTTACTGGGGATGGAACTGGTGAGCTG
||||| ||| || | || ||| |||| ||||| || | | |||| | |||| ||| | || | ||| |||||||||||| || ||||| ||||||| ||| | ||||| ||||||||||| | |||||| |||||||||||||||| ||||||||||||||||||||
gtaagcaagctgcaatattatgatatttttaatatattttatttatacaatgctatcgggagtgactcttgtttgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACAGATGGGTCCTGGTGGTTTATTTTTTACCGGGGATGGAACTGGTGAGCTC
















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|29675454|gb|CB671729.1|CB671729
EST:     CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATC                         GTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
genomic: CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagt ... gggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
EST: gi|218479278|gb|FG957154.1|FG957154
EST:     CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATC                         GTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
genomic: CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagt ... gggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
EST: gi|29618177|gb|CB623189.1|CB623189
EST:     CTACTATGTTCAATAAATGACAACACTGTCCGACTATATGACCTGCCATC                         GTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
genomic: CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagt ... gggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
EST: gi|86501745|gb|CI144378.1|CI144378
EST:     CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATC                         GTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
genomic: CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagt ... gggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
EST: gi|86501991|gb|CI144624.1|CI144624
EST:     CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATC                         GTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
genomic: CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagt ... gggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
EST: gi|86851536|gb|CI314119.1|CI314119
EST:     ACACTGTCCGACTATAT-ATCTGCCATC                         GTTCAGTGATA-GGCCA-GATATTCTCAAAACAGGAAATAAGGGCAATACA
genomic: ACACTGTCCGACTATATGACCTGCCATCgtaagaaagt ... gggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
EST: gi|29657539|gb|CB653814.1|CB653814
EST:     CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATC                         GTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
genomic: CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagt ... gggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
EST: gi|33794977|gb|CF323368.1|CF323368
EST:     CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATC                         GTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
genomic: CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagt ... gggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
EST: gi|58674413|gb|CK063099.1|CK063099
EST:     CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATC                         GTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA
genomic: CTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATCgtaagaaagt ... gggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattttgttttacttctgatgtttatctgaagtggctccttttgggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACAAGTTGGTCCTAGTGGTTTATTTTTTACTGGGGATGGAACTGGTGAGCTG
               ttctgat  putative branch site (score: 3)
 ctccttttg  putative PPT
 tttgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaagttgtcttgctaagattattttgttttacttctgatgtttatctgaagtggctccttttgggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACAAGTTGGTCCTAGTGGTTTATTTTTTACTGGGGATGGAACTGGTGAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA