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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttaatctgccactattgagcgtcttccggccacacttacctcagctcagatgcgcttgtttctcaccattgttgcttgttgaactgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCTTGAGGATTAGCTCTGCTTTCTTTTTTCTGAACCTGGTTACTGCTAGTAC

Basic information

species Oryza sativa
transcript LOC_Os04g28420.1
intron # 11
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|86412554|gb|CI066959.1|CI066959
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|218489779|gb|FG969223.1|FG969223
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|3762939|gb|AU029691.1|AU029691
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTNCCTGGGAAGCAGGAGGCACANCCTATGGCCATTGACAGTNCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|86506588|gb|CI149221.1|CI149221
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|89163178|gb|CI100068.1|CI100068
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|2312019|gb|C28174.1|C28174
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|86484135|gb|CI126768.1|CI126768
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATCGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|86528735|gb|CI168941.1|CI168941
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|86485367|gb|CI128000.1|CI128000
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|89181155|gb|CI045238.1|CI045238
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|88258090|gb|CI360676.1|CI360676
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|89184352|gb|CI046917.1|CI046917
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|86535436|gb|CI175642.1|CI175642
EST:     CATGTTCGCGAAATGGAGGAAGCTGGTACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: CATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|86528371|gb|CI168577.1|CI168577
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|86832739|gb|CI345153.1|CI345153
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|88849661|gb|CI089767.1|CI089767
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|15847220|gb|BI795496.1|BI795496
EST:     CGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACACTGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGT-CCGCT
genomic: CGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACA-TGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|86427218|gb|CI072315.1|CI072315
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         --G-TGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|8527213|gb|AU092028.1|AU092028
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|88989314|gb|CI043813.1|CI043813
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|88907936|gb|CI090532.1|CI090532
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|10794673|gb|AU108639.1|AU108639
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
EST: gi|86483317|gb|CI125950.1|CI125950
EST:     ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAG                         AAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT
genomic: ACGGCAACATGTTCGCGAAATGGAGGAAGCTGGAACACATGGAGAACAAGgtaggttaat ... actgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctcagctcagatgcgcttgtttctcaccattgttgcttgttgaactgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCTTGAGGATTAGCTCTGCTTTCTTTTTTCTGAACCTGGTTACTGCTAGTAC
                      ttctcac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttaatctgccactattgagcgtcttccggccacacttacctcagctcagatgcgcttgtttctcaccattgttgcttgttgaactgctgcagAAGGTGCCTGGGAAGCAGGAGGCACAGCCTATGGCCATTGACAGTGCCGCTTGAGGATTAGCTCTGCTTTCTTTTTTCTGAACCTGGTTACTGCTAGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT