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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagttttgaatgcagatagtagcattagattgttgcctctggttccagtccaagttgctatttcgtagctagtcataagtcataactattttcttctatatcactattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAAAAATTGGCTTGAACCTTTGCCTGATGGTAGCTTGCCAAATATGAATATT

Basic information

species Oryza sativa
transcript LOC_Os01g05420.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G100881_T01 (Zea mays), 3'ss of exon 4
gtaagaagttttgaatgcagatagtagcattagattgttgcctctggttccagtccaagttgctatttcgtagctagtcataagtcataactattttcttctatatcactattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAAAAATTGGCTTGAACCTTTGCCTGATGGTAGCTTGCCAAATATGAATATT
                     ||  |    | || | || ||| | || ||||| ||  |||  |||| ||   |||  || | | |||    |||| || | |||| || |||  |||||||||||| || |||||||| ||||| |||||||||||||||||||||||||| |||||||| || || |||||||| ||| ||||||| ||||||| |
--------------------gtaagatatctggaatctttcctgtagtcccagtgcatattgtcattt-gtttatagctatcaataata----tttttttgtttatctctgtttcacagGAAGAATCTTCAACAGGAATTTCTTGACCATGGAGTTCTCACTCTTCTAAAAAACTGGCTTGAGCCATTACCTGATGGAAGCATGCCAAACATGAATACT

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G085254_T03 (Zea mays), 3'ss of exon 2
gtaagaagttttgaatgcagatagtagcattagattgttgcctctggttccagtccaagttgctat---ttcgtagctagtcataagtcataactat-tttcttctatatcactattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAAAAATTGGCTTGAACCTTTGCCTGATGGTAGCTTGCCAAATATGAATATT
                          | |  | ||           || ||||| ||  |||  ||   ||  |||||   ||   | ||| |  || |||||| | |||| | ||||  |||||||||||| ||||||||||| ||||| || |||||||||||||||||||||||||||||||| || || |||||||| ||| ||||||| |||||||||
--------------------------gtaagatatctggaatctaagtgccagtgcatattgtcatctgtttatagctga-cacctgacattaaaatatttcttgtttatctccatttcacagGAAGAATCTTCAGCAGGAATTTCTTGACCACGGAGTTCTCACTCTTCTAAAAAATTGGCTTGAGCCATTACCTGATGGAAGCATGCCAAACATGAATATT
















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|29665318|gb|CB661593.1|CB661593
EST:     GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAA                         GAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
genomic: GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAAgtaagaagtt ... tattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
EST: gi|29631192|gb|CB636201.1|CB636201
EST:     GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAA                         GAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
genomic: GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAAgtaagaagtt ... tattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
EST: gi|58652440|gb|CK041120.1|CK041120
EST:     GCTATTAATAAACTTATGAAGCTTCCACTAGGCATAGATGTACTCTCAAA                         GAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
genomic: GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAAgtaagaagtt ... tattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
EST: gi|58659042|gb|CK047722.1|CK047722
EST:     GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAA                         GAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
genomic: GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAAgtaagaagtt ... tattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
EST: gi|29670426|gb|CB666701.1|CB666701
EST:     GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAA                         GAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
genomic: GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAAgtaagaagtt ... tattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
EST: gi|29679611|gb|CB675886.1|CB675886
EST:     GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAA                         GAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA
genomic: GCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAAgtaagaagtt ... tattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAA

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), 74 (downstream exon)
Score: 15

TTGAAGTGGCAGCTGAAGAAGATGCCAACTTAAATAGGCAATCAAAACCAGCTATTAATAAACTTATGAAGCTTCCACTACTCATAGATGTACTCTCAAAgtaagaagtt ... tattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAAAAATTGGCTTGAACCTTTGCCTGATGGTAGCTTGCCAAATATGAATATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcgtagctagtcataagtcataactattttcttctatatcactattttgcagGAAGAATCTCCAGCAGGAATTCCTTGATCATGGAGTTCTCACTCTTCTAAAAAATTGGCTTGAACCTTTGCCTGATGGTAGCTTGCCAAATATGAATATT
                    tcataac  putative branch site (score: 15)
                                            ctatttt  putative PPT
                           tattttcttctatat  TA-rich tract