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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatactcattctcatttcagtatttgacccagcttttgttttattatcttctttctccagcatgtttaacacttctttttgttactttgctctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACA

Basic information

species Oryza sativa
transcript LOC_Os02g13990.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G021742_T01 (Zea mays), 3'ss of exon 2
-aatactcattctcatttcagtatttgacccagcttttgttttattatcttctttctccagcatgt-ttaacacttctttttgttactttgctctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACA
 |||| | | | | |  ||  |||||      |  |||  ||  ||   ||| ||||| ||| | | |||||||    | |  | ||| | ||||| || ||||||| |||||||||||||||||||| || |||||||||||||||||||| |||||||| |||||||||||||||||||||||  ||||||| |||||||
gaatagtaaattttaaatct-tatttagaatggtatttagttgtttgggttccttctctagcctttcttaacaccatctatattcactct-ctctctaacagGACCAGTTTGACACAATTGACTTGTCGGATAATGAGATTGTCAAGCTTGAAAACTTCCCATACTTGAATCGTCTTGGCACTCTACTAGTTAATAATAACA

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G18440.2 (Glycine max), 3'ss of exon 3
---------------------------aatactcattctcatttcag----tatttgacccagcttttgttttattatcttctt---tctccagcatgtttaacacttctttttgttactttgc-------tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACA
                           | |   |  |   |||| |     ||| | |    | || | | ||  ||| | |||   |    |  |   || |  ||  | ||  | | |||||       | ||    ||||||||||||||||||| ||||| || |||||||||||||| || ||||| ||  | || ||  | || ||  | |||||  || |  ||||||| ||||
gtgcaaaatttaatcttccttcctttcagtttccccttatatttgaaagtatatattattatgattctctctttatatatgcttcaattataaaaaaacttcatcctggtgttcataaatttgcaatggattttcctgcagGACCAATTTGACACAATAGACTTATCTGACAATGAGATTGTTAAACTTGAAAATGTACCATATCTTAACCGGTTGGGCACAATGCTCATTAACAACAACA

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G24350.2 (Glycine max), 3'ss of exon 3
-------------------------------aatactcattctcatttcag----tatttgacccagcttttgttttattatcttctt--tctccagcatgtttaacacttctttttgttactttgc-------tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACA
                               | |   |  |   |||| |     ||| |      |  | ||| ||  ||| | |||  | |  |  |   || |  ||| | ||  | | |||||       | ||    |||||||||| |||||||| ||||| || ||||||||||||||||| ||||| ||  | || ||  | || ||  | || ||  || |  ||||||| ||||
gtgcacaatttaatcttcttcccttccttttagtttccccttatatttgaaaggatatatcgttatgactctgtcttcatatgtgcttcatttataaaaaaattcatccttgtgttcttaaatttgcaatggattttcctgcagGACCAATTCGACACAATAGACTTATCTGACAATGAGATTGTCAAACTTGAAAATGTACCATATCTTAACCGGTTGGGTACAATGCTCATTAACAACAACA

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 2
aatactcattctcatttcagtatttgacccagcttttgttttattatcttcttt-ctccagcatgtttaacacttctt--tttgttactttgctctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACA
     | |   |  |||||||   |   |  | ||     || || | || |   ||  |   |  ||     | | |  ||| |   |  ||||      ||||||||||||| || ||||| ||||| |||||||||||||||||||| || ||||| || ||  | |||||  | || ||| || |  | ||||| || |
---ctttaaaattgtttcagtggatttacttgtttgcagcttcttgtgttttgcactttaatgttgttgcttttgcatgatttttatatcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA

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|218492413|gb|FG947005.1|FG947005
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|29681478|gb|CB677753.1|CB677753
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|86904173|gb|CI306591.1|CI306591
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|88406774|gb|CI603968.1|CI603968
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|88445434|gb|CI584547.1|CI584547
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCA
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCA
EST: gi|86891922|gb|CI310086.1|CI310086
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|58602112|gb|CK012640.1|CK012640
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|88745945|gb|CI769305.1|CI769305
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACA
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACA
EST: gi|88740329|gb|CI763837.1|CI763837
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGAC
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGAC
EST: gi|88400407|gb|CI593482.1|CI593482
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTTGACACAATTTGACTTGTCAGACAATGAGATTGTCAAGCTTG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTT-GACACAATT-GACTTGTCAGACAATGAGATTGTCAAGCTTG
EST: gi|38473912|gb|CF958044.1|CF958044
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|58662231|gb|CK050911.1|CK050911
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|5005008|gb|AU068325.1|AU068325
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGANACAATT
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttctttctccagcatgtttaacacttctttttgttactttgctctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACA
                  gtttaac  putative branch site (score: 3)
                          cttctttttgttactt  CT-rich tract
                              tttttgtta  TA-rich tract