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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGGTTCACCCTCTGAAGGTTTCTCTGGAGGAATTGTACAATGGCACATCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatcagcttccttttgtgggtcctaaatattgcataaactgtttgactattctgatatctcacactgttctgtgctcatcttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g57340.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57340.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G17930.1 (Glycine max), 5'ss of exon 3
ATGTGGTTCACCCTCTGAAGGTTTCTCTGGAGGAATTGTACAATGGCACATCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtca--tcagcttccttttgtgggtcctaaatattgcataaactgtttgactattctgatatctcacactgttctgtgctcatcttgcag--------
|||||||||||||||| ||||| |||||||||||  | ||    || || || |||||||||||||| ||  | |||||  | ||||||||||||| |||||  || |  ||||  |    |||  | |  || || ||    |||   |   | |  | || | |   |   || | | |  | ||    |          
ATGTGGTTCACCCTCTCAAGGTCTCTCTGGAGGACCTTTATCTCGGGACTTCTAAGAAGCTCTCCCTCTCCAGAAATGTCATATGCTCCAAGTGCACTGGgtgagtgaattcagagtttgcttggtgat--tagattttaggaaaaaattactatttgtttggtttaaaattatgatgtttattaatacgacgtagcatggt

upper sequence: LOC_Os03g57340.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0073g00560.t01 (Vitis vinifera), 5'ss of exon 4
ATGTGGTTCACCCTCTGAAGGTTTCTCTGGAGGAATTGTACAATGGCACATCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgt------cat-cagcttccttttgtgggtcctaaatattgcataaactgtttgactattctgatatctcacactgttctgtgctc--------atcttgcag
| ||  | ||||| || |||||||||||||| ||  | |||||||| ||||| ||||| || ||||||||||| |||||  ||||||| |||||||| ||||  ||       || |||  | ||    |   | |    |  ||  |  |   | ||||| |  |  |  || | | |||    || |         |  ||||||
ACGTCATCCACCCCCTTAAGGTTTCTCTGGAAGATCTCTACAATGGGACATCCAAGAAACTGTCCCTTTCTCGTAATGTAATCTGCTCAAAGTGCAAGGGgtgagtacaaactatgcagtattctcagttttctgcagtttcgtgtctgcatcttatgactttgtttgtgacttatattgtatcatgattggggtgataatttgcag
















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|58686504|gb|CK075191.1|CK075191
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCAAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|44677099|gb|CR290533.1|CR290533
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAATGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|38472777|gb|CF956909.1|CF956909
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCAAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|701938|gb|D48229.1|D48229
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|29680484|gb|CB676759.1|CB676759
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|218478439|gb|FG959047.1|FG959047
EST:     CTCCCTTTCTCGCAATGTCCTCTG-TCCAA-TGCAATGG                         CAAGGGCTCAAAATCTAGGTGCTTCCATGAAATGCTCTGGTTGTCAAGGTT
genomic: CTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCT-GGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTT
EST: gi|218479625|gb|FG945756.1|FG945756
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         C-AGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|7168829|gb|AU065478.2|AU065478
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|2311036|gb|C27191.1|C27191
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCGAAATCTTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTT
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCT-GGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTT
EST: gi|218502146|gb|FG950394.1|FG950394
EST:     TCAA-GAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CCATGGCTCGAAATCTGGTGCTTCCATGACGTGCTCTGGTTGT
genomic: -CAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGT
EST: gi|58658806|gb|CK047486.1|CK047486
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCAAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|218499104|gb|FG960771.1|FG960771
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCAAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|218495063|gb|FG965805.1|FG965805
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
EST: gi|29686423|gb|CB682698.1|CB682698
EST:     TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGG                         CAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTC

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: 208

ATGTGGTTCACCCTCTGAAGGTTTCTCTGGAGGAATTGTACAATGGCACATCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatc ... catcttgcagCAAGGGCTCGAAATCTGGTGCTTCCATGAAGTGCTCTGGTTGTCAAGGTTCTGGTATGAAGGTCCAAATTCGCCAGTTGGGGCCAGGAATGATTCAGCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGGTTCACCCTCTGAAGGTTTCTCTGGAGGAATTGTACAATGGCACATCAAAGAAGCTCTCCCTTTCTCGCAATGTGCTCTGCTCCAAGTGCAATGGgtatgtcatcagcttccttttgtgggtcctaaatattgcataaactgtttgactattctgatatctcacactgttctgtgctcatcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC