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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGGTTGTAGTCGGGAAAGACTCAACACTAATTGTTACCGATGGAAGCACCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagtccaaaaatttgatgaataacattgtcgttcgaccttcttaacatattaacttacatgccctgttaatgttaaaaaaacttacgtgtcata...

Basic information

species Oryza sativa
transcript 13113.m00214
intron # 7
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|58689939|gb|CK078626.1|CK078626
EST:     CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|58588707|gb|CF987015.1|CF987015
EST:     CCCAACATGTGATCGAGAAAAGGGTTGCTCAGAT-AAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|58687450|gb|CK076137.1|CK076137
EST:     GAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: GAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|58688418|gb|CK077105.1|CK077105
EST:     CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|58692944|gb|CK081631.1|CK081631
EST:     CCCAGCATGTGATTGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAG
EST: gi|29638632|gb|CB643641.1|CB643641
EST:     CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|33681193|gb|CF309432.1|CF309432
EST:     CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|58612906|gb|CK040618.1|CK040618
EST:     CCCAGCATGTGATTGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|33681075|gb|CF309314.1|CF309314
EST:     CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|58689718|gb|CK078405.1|CK078405
EST:     CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|29668896|gb|CB665171.1|CB665171
EST:     CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
EST: gi|58691639|gb|CK080326.1|CK080326
EST:     CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATCAAGGGCCAAATTGAG                         AACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG
genomic: CCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGG

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: 69 (upstream exon), 66 (downstream exon)
Score: 7

TAAGGTTGTAGTCGGGAAAGACTCAACACTAATTGTTACCGATGGAAGCACCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagt ... gaacttccagAACTCAAGTGAGAGGTACCAGAAGAAGATATTGGGTGAGAGAATAGCAAGGTTATGTGGTGGAATTGCAATCATTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGGTTGTAGTCGGGAAAGACTCAACACTAATTGTTACCGATGGAAGCACCCAACATGTGATCGAGAAAAGGGTTGCTCAGATAAAGGGCCAAATTGAGgtattacagtccaaaaatttgatgaataacattgtcgttcgaccttcttaacatattaacttacatgccctgttaatgttaaaaaaacttacgtgtcata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa