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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttttttatctctactaatcaatttgagctttgaggtagatagtaagttcaggaaccctgatgacattggcaatttttttttctgacgcaagtt...

Basic information

species Oryza sativa
transcript LOC_Os01g55570.1
intron # 2
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:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33813231|gb|CF332506.1|CF332506
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88346141|gb|CI634014.1|CI634014
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|55409935|gb|CV722311.1|CV722311
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88573876|gb|CI665645.1|CI665645
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|14714366|gb|AU198287.1|AU198287
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33813229|gb|CF332505.1|CF332505
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33681227|gb|CF309466.1|CF309466
EST:     AGTTCTAGAACCGTCAATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAAAATTTGCAGGG
genomic: AGTTC-AGAACCGTC-ATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33666134|gb|CF297101.1|CF297101
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|86903736|gb|CI300590.1|CI300590
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|38479869|gb|CF963958.1|CF963958
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCACTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|55410151|gb|CV722527.1|CV722527
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88979638|gb|CI026024.1|CI026024
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33681228|gb|CF309467.1|CF309467
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAAAATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88977491|gb|CI025227.1|CI025227
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88988709|gb|CI039128.1|CI039128
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88979318|gb|CI025820.1|CI025820
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88348094|gb|CI637555.1|CI637555
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|38476046|gb|CF960179.1|CF960179
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTGGTGAAGTATGTCCAGAGTTCG                         TTCAGCACTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88574306|gb|CI666075.1|CI666075
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|29686441|gb|CB682716.1|CB682716
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33824040|gb|CF337833.1|CF337833
EST:     ACGGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88342540|gb|CI637116.1|CI637116
EST:     ACAGTTCAAAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAAACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|699911|gb|D46202.1|D46202
EST:     ACAGTTCAGNACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33818515|gb|CF335088.1|CF335088
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33824042|gb|CF337834.1|CF337834
EST:     GAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: GAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|3768522|gb|AU032549.1|AU032549
EST:     AGTTCCAGAACCGTCATCCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCCAGG
genomic: AGTT-CAGAACCGTCAT-CCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTG-CAGG
EST: gi|88368616|gb|CI648094.1|CI648094
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88963183|gb|CI026856.1|CI026856
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|58590453|gb|CF988761.1|CF988761
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCACTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|117225508|gb|CT859158.1|CT859158
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCACTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88296188|gb|CI667578.1|CI667578
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|112785712|gb|EE591260.1|EE591260
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|58587351|gb|CF985659.1|CF985659
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGGGAAGTATGTCCAGAGTTCG                         TTCAGCACTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33672558|gb|CF300797.1|CF300797
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGG-
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33677215|gb|CF305454.1|CF305454
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG

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: 74 (upstream exon), 73 (downstream exon)
Score: 69

GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGGATTGCCGCATTATGGGCTTCTATAAATCTTGTAGAG




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