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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA

Basic information

species Oryza sativa
transcript LOC_Os02g47860.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143804_T01 (Zea mays), 3'ss of exon 1
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaa---agatcttaatacaaaccaaacattcatttcgcaat-ttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
     | || |    |   |  || ||   | |     ||   | |   | |    | | |     | || |  |      |   |||        ||||| || |  ||  | |  | |||   ||     |   | |   | || |      || || |||| ||||||| |||||||||  ||||| ||||||||||| || ||||| || ||||| |||||||| ||||| || |||||||||||||||| |||||| |||||||||||||
----gtacaacgagctagccaggaacccgaagaaataattgatcaaatctctcaaacgataggttgaaatttccaacttggctttacacattaggagcaatcttgtggttcatgttaacagtgaattggctcttactgtaattggtgtggtttaatcaaagatgacattttt-agGTTTATCTAATGTACAAGGCTTTCATCGAACCAGATTTACAGACCGCACATATTAAAATCATTAACAAGTTCAACCCATGCTCAGGTTTCCAAAATCCTA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 4
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                            ||  ||   ||| | |||     ||  | |       | ||   || | |   |  ||  ||   | ||  | || || || |    ||  |||| ||||||  | ||     ||| |||||||||||||||||| ||||| ||||||||||| || ||||| ||| |||| |||||||| || || |||||||||||||||||||| |||||||||||||||||||
-------------------------------------------gtaggttgaattttc-caacttggctatacattttatgagca---atgttgttgtccattgttaaca-gtgaattacctcttactgtaattggtgtggtttaatgaaat-----atgacatttttcagGTTTATCCAATGTACAAGGCTTTCATCGAACCAGATTTGGAGACCGCACATATTAAGATCATCAACAAGTTCAACCCATTTTCAGGGTTCCAAAATCCTA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G14110.1 (Glycine max), 3'ss of exon 4
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                                                                     |||||      ||   |  ||||    | |  ||    |||     || ||||||     |   | | ||   |     ||||||||| ||||| ||||| ||||| || || ||||||||  | ||||||||||| |||||||| |||||||| ||||| |||||  | || ||||| | |||||
------------------------------------------------------------------------------------gttcatacgtttataattcctttggtctttttatacagatttggaaaatatgtgtttccagaagtgcttaagtttaaacattttcagGTGTATCCAATGTACAAGGCATTTATCGAGCCAGATCTCCAGACAGCACACATAAAAATCATCAACAAATTCAATCCATTTACTGGATTCCAGAGTCCTA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G09080.1 (Glycine max), 3'ss of exon 4
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaattt--atattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                                     ||| |||    ||||| |    | |      |||  ||| | | |||  | |  ||| || | ||  | ||    || |   || |  | |||||| |  ||     |  | |||| ||||| ||||| |||||||| ||||| |||||||||||  |  | ||||| ||| ||||||| || |||||||| || |||||||| || ||||| ||||| |
---------------------------------------------------gtttttcact---gatctcatgttata------atttttttaggacttttgaaaacttgcatctgtaaga-ctaaggcacctg-ctataatttttaactat-tgttttgtttccttttgcagGTGTATCCTATGTATAAAGCTTTTATTGAGCCAGATCTCAAAACAGCTCATCTAAAAATTATTAACAAGTTTAATCCATTCTCTGGATTCCAGAATCCCA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G09660.1 (Glycine max), 3'ss of exon 4
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                                                                   ||| | |||   ||||  | |  | | | ||||  |  |||   |   |||||| ||  |  |   | | ||   |     ||||||||| ||||| ||||| ||||| || || ||||||||  | |||||||||||||||||||| |||||||| ||||| |||||  | || ||||| | |||||
--------------------------------------------------------------------------------gttcatac-ttttataattcctttcatctttttata-cagatttagaaaatatctgtatttctagaagtgcttaagtttaaacattttcagGTGTATCCAATGTACAAGGCATTTATCGAGCCAGATCTCCAGACAGCACATATAAAAATCATCAACAAATTCAATCCATTTACTGGATTCCAGAGTCCTA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 3
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatc---catctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                 ||  |||| | |||  | ||||      |||| | |   |||  |   |||  | ||        ||| ||| |  || || || || | ||  |     |||| |  || ||| |||                    ||||| ||||| ||||| |||||||| |||||||||||  | || ||||||||||||||||| |||||||| ||||| |||||| | || || || || || |
--------------------------------gtgt-tttcacttatactatgtta----gaaagttttctttacttaatgaactgttatggtagccctta-attattcatataaagcatttattgtacttctcatcagctttcttttaca--------------------cagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0010g01080.t01 (Vitis vinifera), 3'ss of exon 3
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                                                  |  |   ||  |||      | | | |||   |||    || |   |  | | |  ||||||   || |       | ||| | ||           ||   ||||| ||||| ||||| |||||||| |||||||||||  |    ||||||||||||||||| | ||| ||||||||||||||| | || || || | ||| |
-----------------------------------------------------------------gttctttcacttaccctctgctaaatacgccccttaagaattttgactggattttgcttttcaagaattt------ctcaactacatt-------cttttaaacagGTATATCCAATGTACAAGGCTTTTATTGAGCCAGATCTCGGAACAGCACATATAAAAATCACCAATAAGTTCAACCCATTCACTGGATTTCAGAGTCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                        gtttaac  putative branch site (score: 3)
                                             catttttc  putative PPT
     tttttcat  TA-rich tract