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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTCTCTCTCTGTTCCTTCTATTCAAGTTTCTCTCGAAAGACTTGGTCAATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaaactctccttggaagagctttttcattcatgtaactacttaatactgtatctgtgcaattaagattgttcatgtgcttattttttttctgatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g02530.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02530.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 4
TGCTTCTCTCTCTGTTCCTTCTATTCAAGTTTCTCTCGAAAGACTTGGTCAATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaaactct-----ccttggaa--gagctttttcattcatgtaactacttaatactgtatctgtgcaattaagattgttcatgtgc-ttattttttttctgat----gcag
||||  | || || |||||||| ||||||||||| || ||||||||||| |||||||| || ||   |||||| ||  | ||||| ||   |||||| | ||| || |   |  |      | ||  |    ||||  |  || || ||| || |||  | |   |   ||   ||  | |  ||      | |||| ||| ||||  |    | ||
TGCTGTTATCACTATTCCTTCTCTTCAAGTTTCTATCAAAAGACTTGGTTAATGCTGTACTGACATGCTACTTCTTTGTGCTTGGGATCATCGCTCTTTCgtatgttctttccgtatggatcatgctactatgcttaatatttgatataattatttagaaatagtttcatgtggtttggttcattatctcacattatctttcttctattttctgtag
















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|29629871|gb|CB634880.1|CB634880
EST:     AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTG                         TGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAA-GAATGGAATGA
genomic: AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaa ... tctgatgcagTGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA
EST: gi|58684751|gb|CK073438.1|CK073438
EST:     TTGCCGCTCTCTG                         TGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA
genomic: TTGCCGCTCTCTGgtaagtccaa ... tctgatgcagTGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA
EST: gi|58590779|gb|CF989087.1|CF989087
EST:     AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTG                         TGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA
genomic: AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaa ... tctgatgcagTGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA
EST: gi|701074|gb|D47365.1|D47365
EST:     AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTG                         TGCA-CATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA
genomic: AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaa ... tctgatgcagTGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA
EST: gi|701106|gb|D47397.1|D47397
EST:     AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTG                         TGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGGAATT
genomic: AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaa ... tctgatgcagTGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGG-AATG
EST: gi|701499|gb|D47790.1|D47790
EST:     AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTG                         TGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATAA
genomic: AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaa ... tctgatgcagTGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA
EST: gi|58674882|gb|CK063569.1|CK063569
EST:     AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTG                         TGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA
genomic: AATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaa ... tctgatgcagTGCAACATTGCTGCCTTCCATAAAACGATTCCTTCCAAAAGAATGGAATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTCTCTCTCTGTTCCTTCTATTCAAGTTTCTCTCGAAAGACTTGGTCAATGCTGTTCTCACTGCCTACTTTTTCATCCTTGGCATTGCCGCTCTCTGgtaagtccaaactctccttggaagagctttttcattcatgtaactacttaatactgtatctgtgcaattaagattgttcatgtgcttattttttttctgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT