Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgtaatcgccatatatcacacttgcaaaagtttacatggatctgtttgagaaatggctccatttctgtatatttacatagcagatgcttccaa...

Basic information

species Oryza sativa
transcript LOC_Os01g55570.1
intron # 5
splice site 5'
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|33818625|gb|CF335136.1|CF335136
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33813231|gb|CF332506.1|CF332506
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88515407|gb|CI443061.1|CI443061
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88663053|gb|CI477731.1|CI477731
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|58030284|gb|CX727827.1|CX727827
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTTTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88991906|gb|CI035044.1|CI035044
EST:     TTGTTCATATATCGAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACTACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33666135|gb|CF297102.1|CF297102
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTTTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88514875|gb|CI442529.1|CI442529
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88502246|gb|CI429752.1|CI429752
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88286237|gb|CI522537.1|CI522537
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAA                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCTTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33813229|gb|CF332505.1|CF332505
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33681227|gb|CF309466.1|CF309466
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTTTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33666134|gb|CF297101.1|CF297101
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|38479869|gb|CF963958.1|CF963958
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|55410151|gb|CV722527.1|CV722527
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGG
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGG
EST: gi|88979638|gb|CI026024.1|CI026024
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33681228|gb|CF309467.1|CF309467
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88977491|gb|CI025227.1|CI025227
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88661619|gb|CI457276.1|CI457276
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88988709|gb|CI039128.1|CI039128
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88979318|gb|CI025820.1|CI025820
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88471188|gb|CI408459.1|CI408459
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|38476046|gb|CF960179.1|CF960179
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|29686441|gb|CB682716.1|CB682716
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33824040|gb|CF337833.1|CF337833
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|699911|gb|D46202.1|D46202
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33818515|gb|CF335088.1|CF335088
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTTTGAACAACATCAAGAGTTCCGTATTTCGCGTTTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33824042|gb|CF337834.1|CF337834
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88663661|gb|CI484642.1|CI484642
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88463041|gb|CI522152.1|CI522152
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|3768522|gb|AU032549.1|AU032549
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88963183|gb|CI026856.1|CI026856
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|58590453|gb|CF988761.1|CF988761
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAACAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|117225508|gb|CT859158.1|CT859158
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|112785712|gb|EE591260.1|EE591260
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGGC
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGG-C
EST: gi|88662023|gb|CI462779.1|CI462779
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|88517883|gb|CI444859.1|CI444859
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTGTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|58587351|gb|CF985659.1|CF985659
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
EST: gi|33677215|gb|CF305454.1|CF305454
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTCCTGAACA-CATCAAGAGTTCCGTATCTCGCGTC
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTC
EST: gi|88662192|gb|CI466141.1|CI466141
EST:     TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAG                         GGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA
genomic: TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCA

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: 38 (upstream exon), 73 (downstream exon)
Score: 81

TTGTTCATATATCAAAACCTACTATTCAAGCCAGACAGgtaactttgt ... ttttctgcagGGAAAAGTTTCTGAACAACATCAAGAGTTCCGTATCTCGCGTCTTGGGGCAGTAATTTGAGGCGAAAATGGAGCACAAGCAGCCTTAACTCTTGCCGTCG




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