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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagccacctctctctctttgtctgtgtgtgtttcttgcgtttgtcctgagatgaagatcgttgtgccctgtgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGCGGGCTGGGGTGCGAGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGA

Basic information

species Oryza sativa
transcript LOC_Os01g16540.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G007915_T02 (Zea mays), 3'ss of exon 1
----gtcagccacctctctctctttgtctgtgtgtgtttcttgcgtttgtcct-----gagatgaagatcgttg--tgccctgtgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGCGGGCTGGGGTGCGAGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGA
    ||   |   |      |  |  || || | | ||||| |||||  | ||     | |||  |  ||||||  ||  | | ||| |||||||||| |||   ||||||||||||||||||||  |||| ||||||||||||||||| || ||||||||||||||||||||||| |||||||| || ||||
gtgagtggactggcgtcgatttctcctccgt-tttttttctcgcgttcttacttctaagcgattgatctcgttgattgatccgcgcg-cgcagCTGCGAGACCTACTGGGGAGCCTCGTGGAGGTTTTGGTTGTGGGCGCGGGCGGGCTTGGCTGCGAGCTCCTCAAGGACCTGGCTCTCTCCGGGTTTAAGA
















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|88404494|gb|CI580930.1|CI580930
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|29634620|gb|CB639629.1|CB639629
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88352497|gb|CI615751.1|CI615751
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88391799|gb|CI603318.1|CI603318
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|7168814|gb|C28508.2|C28508
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88414839|gb|CI604197.1|CI604197
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88313796|gb|CI597427.1|CI597427
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88299111|gb|CI570081.1|CI570081
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88390471|gb|CI607507.1|CI607507
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88337432|gb|CI630729.1|CI630729
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88726387|gb|CI750042.1|CI750042
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88359773|gb|CI622463.1|CI622463
EST:     TCTCCCGCCCCGGAAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88360510|gb|CI608362.1|CI608362
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|58612567|gb|CK040279.1|CK040279
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|58594978|gb|CF993286.1|CF993286
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88396406|gb|CI598518.1|CI598518
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|58655476|gb|CK044156.1|CK044156
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88403087|gb|CI568861.1|CI568861
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88372622|gb|CI612550.1|CI612550
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|88391890|gb|CI603409.1|CI603409
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|58661497|gb|CK050177.1|CK050177
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
EST: gi|66915301|gb|CX102149.1|CX102149
EST:     TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGG                         CTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC
genomic: TCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGC

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: 23 (upstream exon), 71 (downstream exon)
Score: 2

CGAGGACCCGCCGACGGAGCCCGAGCGGTGGAGGGATCTGGACATGCTCCTCTCCCGCCCCGGCAACCTCGTCCACGCCGACTTCAACCCCAGCCCCGGGgtcagccacc ... tgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGCGGGCTGGGGTGCGAGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagccacctctctctctttgtctgtgtgtgtttcttgcgtttgtcctgagatgaagatcgttgtgccctgtgcgtcgcagCTGCGGGACTCGCTGGGGAGCCTCGTGGAGGTGCTGGTGGTGGGCGCGGGCGGGCTGGGGTGCGAGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC