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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaataactagtgtatgagaaattcaccatttccgaggattgttgctgggtttactcatgctaatatctgagaaatttaccacctgtctgattgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG

Basic information

species Oryza sativa
transcript LOC_Os01g74650.1
intron # 7
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|58678120|gb|CK066807.1|CK066807
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|701729|gb|D48020.1|D48020
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTNAG                         ATATCTAGTGATGAGGCTGTTTGAGACAGCAAAGCAATTGGCTCTTCCAGG
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTT-GAGACAGCAAAGCAATTGGCTCTTC-AGG
EST: gi|86413547|gb|CI019132.1|CI019132
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29655936|gb|CB652211.1|CB652211
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|58691812|gb|CK080499.1|CK080499
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29616466|gb|CB621478.1|CB621478
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29663371|gb|CB659646.1|CB659646
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29687246|gb|CB683521.1|CB683521
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|163927355|gb|EG710663.1|EG710663
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|84117136|gb|CD150903.1|CD150903
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTTAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|33801701|gb|CF326722.1|CF326722
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|38480498|gb|CF964587.1|CF964587
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|86494722|gb|CI137355.1|CI137355
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29655935|gb|CB652210.1|CB652210
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|88847644|gb|CI018335.1|CI018335
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCGAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|38469869|gb|CF954000.1|CF954000
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29672976|gb|CB669251.1|CB669251
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29677863|gb|CB674138.1|CB674138
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|87008043|gb|CI297021.1|CI297021
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGC
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGC
EST: gi|58690422|gb|CK079109.1|CK079109
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|88845335|gb|CI084260.1|CI084260
EST:     GAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29616196|gb|CB621208.1|CB621208
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|58696201|gb|CK084888.1|CK084888
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|86535476|gb|CI175682.1|CI175682
EST:     CTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: CTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|38471318|gb|CF955449.1|CF955449
EST:     GTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTATTGATGAGGCTGTTGAGACAGCAAGAGCAATTGGCTCTTCAGGA
genomic: GTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAA-AGCAATTGGCTCTTCAGGA
EST: gi|88220621|gb|CI220181.1|CI220181
EST:     TGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: TGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29644300|gb|CB649307.1|CB649307
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|13420475|gb|AU174565.1|AU174565
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|300215770|gb|HO088396.1|HO088396
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGTGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|29684900|gb|CB681175.1|CB681175
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|86417511|gb|CI031720.1|CI031720
EST:     TCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: TCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
EST: gi|88387705|gb|CI585408.1|CI585408
EST:     GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAG                         ATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA
genomic: GATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAA

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: 43 (upstream exon), 33 (downstream exon)
Score: 1

GCCCACATAAGATTCAAGGCATTGGGGCAGGATTTGTTCCAAGGAACTTGGATAGTGAAGTTCTCGATGAAGTGATTGAGgtctgcactt ... attgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgggtttactcatgctaatatctgagaaatttaccacctgtctgattgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG
                         agaaattta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaataactagtgtatgagaaattcaccatttccgaggattgttgctgggtttactcatgctaatatctgagaaatttaccacctgtctgattgttgcagATATCTAGTGATGAGGCTGTTGAGACAGCAAAGCAATTGGCTCTTCAGGAAGGATTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - gtgtatg
- - - - - - - - - - - ttcacca
- - - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgtct