Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactatctccttcactctagctctttggatatgtttagattccacttagatctgcttaatttggattgcctgtcattcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG

Basic information

species Oryza sativa
transcript LOC_Os07g49270.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 16
gtaactatctccttcactctagctctttggatatgttta---gattccacttagatctgcttaatttggattgcctgtcattcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG
      ||  || |  ||||| |||| |  || |||||     || ||||  |||  | |||| | |||||||| |||   ||||||||||| |||||||| || ||||| ||| | |||||||| ||||| |||||||| |||||||| || |||||||| |||||||||
---gtaatgcccctatctctatctctgtc-atgtgttttcccaatcccacccagaggttcttagtctggattgcttgttgctcttggcagCTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG
















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|58694980|gb|CK083667.1|CK083667
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|29671781|gb|CB668056.1|CB668056
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|86481989|gb|CI124622.1|CI124622
EST:     GCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: GCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|86437389|gb|CI119111.1|CI119111
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|89169860|gb|CI110219.1|CI110219
EST:     TGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|33675288|gb|CF303527.1|CF303527
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|29663749|gb|CB660024.1|CB660024
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGA
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGA
EST: gi|29663750|gb|CB660025.1|CB660025
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|86478852|gb|CI121485.1|CI121485
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|8527210|gb|AU092025.1|AU092025
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCT-NTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|86437366|gb|CI119088.1|CI119088
EST:     TGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|88966319|gb|CI119454.1|CI119454
EST:     AATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: AATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|58695027|gb|CK083714.1|CK083714
EST:     TTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|218478545|gb|FG960299.1|FG960299
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGACTATAGCATCGCTGCTTCG                         CTGTGGAAGCTACGTTCATGCGCAC-TATGTGAAATTGCTAGGAATTCTGT
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCG-ACCTATGTGAAATTGCTAGGAATTCTGT
EST: gi|163927650|gb|EG712446.1|EG712446
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|86481726|gb|CI124359.1|CI124359
EST:     ATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCGATGTGAAATTGCTAGGAATTCTGTG
genomic: ATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|58593125|gb|CF991433.1|CF991433
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|86477298|gb|CI119931.1|CI119931
EST:     ATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: ATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|163926592|gb|EG713608.1|EG713608
EST:     TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
EST: gi|87027426|gb|CI272191.1|CI272191
EST:     TCGCTGCTTCG                         CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG
genomic: TCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTG

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: 74 (upstream exon), 67 (downstream exon)
Score: 23

TTTCCTAAGAGGCCTTAACGTTTCTCTATCAACCGATGACCCTTTGCAAATTCACCTGACAAAAGAACCTTTGGTTGAAGAATATAGCATCGCTGCTTCGgtaactatct ... ttcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttagattccacttagatctgcttaatttggattgcctgtcattcttggcagCTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG
                       gcttaat  putative branch site (score: 23)
                                          tcattctt  putative PPT
                         ttaattt  TA-rich tract