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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatggtaatgtaccttatatgaatattgtagttagagaagtattttatttaacttttctctgttatgttggggcataacacaatctatctttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG

Basic information

species Oryza sativa
transcript LOC_Os04g23890.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 12
--------------------------------------------------------------------aaatggtaatgtaccttatatgaatattgtagttagagaagtattttatttaacttttc-tctgttatgttgg--ggcataacacaatctatctttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG
                                                                      ||  | || |   ||  ||   | |   | ||  |||||  |   ||     ||||| || ||||| ||    |   |   |  |    | | |||  ||||||||||| ||||||||||||||||| ||    |  || | ||||  |||||||||   | | || |||||||||||||| ||| |||||
gtaaggtattcattccttttgggttatcaataccctacctatgtatacattttcagatttccttgaatgcattattatatgtttttcatagttgtgtcatttgaagaagggtggaatggtgtttttcatcagttatatttaatgatgtcgtatgaatcttttatgttgcagAGACCAGAAGATTTGTGGGCAATTCATTCCCAACCCGTCTTTCCACGACCTCACAAGAAGGAAAATCCTTCTTGGATAGCGATACAAAAG

upper sequence: LOC_Os04g23890.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G33560.2 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------aaatggtaatgtaccttatatgaatattgtagttagagaagtattttatttaacttttctctgttatgttggggcataacaca---atctatctttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG----------
                                                                 ||  |  | |   ||  ||   | |  |    |||  |||  |  |  |   |||| || ||||| || |   ||| || |   |||| | |||||  ||||||||||| ||||||||||||||||| ||    | ||| | ||||  ||||||||||  | | || |||||||||||||| ||| |||||          
gtattcctttttttgggttagcaacaccctacctatgcatatatttttcagatttcctttaatgcattattttatgtttttcatagctgtcatttgaagaagagtggta-aggtgctttttgtcagttatatttgatgatatcatatgaatctgt-tttgttgcagAGACCAGAAGATTTGTGGGCAATTCATTCCCAACCTGTCTTTCCACGACCTCACAAAAAGGACAATCCTTCTTGGATAGCAATACAAAAGGTACCAATTT

upper sequence: LOC_Os04g23890.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G33560.1 (Glycine max), 3'ss of exon 10
--------------------------------------------------------------------aaatggtaatgtaccttatatgaatattgtagttagagaagtattttatttaacttttctctgttatgttggggcataacaca---atctatctttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG----------
                                                                      ||  |  | |   ||  ||   | |  |    |||  |||  |  |  |   |||| || ||||| || |   ||| || |   |||| | |||||  ||||||||||| ||||||||||||||||| ||    | ||| | ||||  ||||||||||  | | || |||||||||||||| ||| |||||          
gtaaggtattcctttttttgggttagcaacaccctacctatgcatatatttttcagatttcctttaatgcattattttatgtttttcatagctgtcatttgaagaagagtggta-aggtgctttttgtcagttatatttgatgatatcatatgaatctgt-tttgttgcagAGACCAGAAGATTTGTGGGCAATTCATTCCCAACCTGTCTTTCCACGACCTCACAAAAAGGACAATCCTTCTTGGATAGCAATACAAAAGGTACCAATTT

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|29612810|gb|CB617823.1|CB617823
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
EST: gi|14571435|gb|BI118803.1|BI118803
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
EST: gi|29666947|gb|CB663222.1|CB663222
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
EST: gi|58587914|gb|CF986222.1|CF986222
EST:     CAGCGGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
EST: gi|29615865|gb|CB620877.1|CB620877
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
EST: gi|29686409|gb|CB682684.1|CB682684
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
EST: gi|29680789|gb|CB677064.1|CB677064
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
EST: gi|29613843|gb|CB618856.1|CB618856
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         G
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcag-
EST: gi|29613843|gb|CB618856.1|CB618856
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         G
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcag-
EST: gi|29613843|gb|CB618856.1|CB618856
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         G
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcag-
EST: gi|29684157|gb|CB680432.1|CB680432
EST:     CAGCACCCAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGCTGTTTCTCCAAAACC
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCG-TGTTTCTCCAAAACC
EST: gi|29646469|gb|CB651476.1|CB651476
EST:     CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTG                         AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT
genomic: CAGCAGAGAATGTGGATGATGCAGTCAGGGAGCTTCCTGATGCCAACTTGgtaaggtaca ... tttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttaacttttctctgttatgttggggcataacacaatctatctttgtctcagAGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG
                            gcataac  putative branch site (score: 3)
                                       tctatctttgtctc  putative PPT
     taactttt  TA-rich tract