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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_Os02g13990.1
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|86904173|gb|CI306591.1|CI306591
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|29660695|gb|CB656970.1|CB656970
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
EST: gi|27553936|gb|CA997836.1|CA997836
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|29663404|gb|CB659679.1|CB659679
EST:     GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG                         GACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
genomic: GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAG
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

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), 51 (downstream exon)
Score: 52

GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAGgtgagctcca ... tctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttctttctccagcatgtttaacacttctttttgttactttgctctcaaatagGACCAATTTGACACAATTGACTTGTCAGACAATGAGATTGTCAAGCTTGAGAACTTCCCGTACTTGAATCGTCTTGGCACTCTGTTAGTTAACAATAACA
                  gtttaac  putative branch site (score: 52)
                          cttctttttgttactt  CT-rich tract
                              tttttgtta  TA-rich tract