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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaaccacttgtgttgtttgagccatgatatttttagtttcaccacaatatattcttatagaataaatttccactgttctgtttgttgccctctaaattaaaccaaaatgtatggattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 10
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|58656234|gb|CK044914.1|CK044914
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|218490049|gb|FG963619.1|FG963619
EST:     CTTG-TTTC-ATGATGATATCCA-                         GGAACA-CATCTGTGGTCCTT-CA-GTCTTTTATCATCACTAAAGGTGGTT
genomic: CTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|33676232|gb|CF304471.1|CF304471
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|29642462|gb|CB647469.1|CB647469
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|218495881|gb|FG947063.1|FG947063
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|58608599|gb|CK036632.1|CK036632
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|29645565|gb|CB650572.1|CB650572
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|86848740|gb|CI294021.1|CI294021
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|33676868|gb|CF305107.1|CF305107
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|14192240|gb|AU184451.1|AU184451
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|33793137|gb|CF322449.1|CF322449
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATC
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATC
EST: gi|58670000|gb|CK058686.1|CK058686
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|58672496|gb|CK061182.1|CK061182
EST:     GAGTCATCTTGTTTTCAATGATGATATCCAC                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: GAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|58681408|gb|CK070095.1|CK070095
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|58607251|gb|CK035284.1|CK035284
EST:     GCAAAATACAGCAAGAGTCATC-TGTTTTCAATGATGATATCCAC                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: GCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|58671508|gb|CK060194.1|CK060194
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|218499296|gb|FG965743.1|FG965743
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|58665642|gb|CK054328.1|CK054328
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|33676662|gb|CF304901.1|CF304901
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
EST: gi|58597534|gb|CK008062.1|CK008062
EST:     TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAG                         GGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT
genomic: TGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTT

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: 75 (upstream exon), 75 (downstream exon)
Score: 61

TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaac ... tggattgcagGGAACAGCATCTGTGGTCCTTGCAGGTCTTTTATCATCACTAAAGGTGGTTGGTGGAACCCTGGCTGAACACACTTATTTGTTCCTTGGTGCTGGTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGAGGACTTCGCCAATCACAACGCATTTGATTTGCTTGCAAAATACAGCAAGAGTCATCTTGTTTTCAATGATGATATCCAGgtaaatgaaccacttgtgttgtttgagccatgatatttttagtttcaccacaatatattcttatagaataaatttccactgttctgtttgttgccctctaaattaaaccaaaatgtatggattgcag

- - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA