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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcactcttctgaatgtatgatgtgttttatagtttgcaccgttaacgactcttttctctacacttccacaggagcatgctaatggtggaaaatgtattgtgtttactcaaactaaacgagagGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGCTTCATGGGGATATTTCACAGAATCAGAGAGAAAGGACACTATCAGGATTTC

Basic information

species Oryza sativa
transcript LOC_Os07g05050.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g05050.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------gtgagcactct-tctgaatgtatgatgtgttttatagtttgcaccgttaacgactcttttctctacacttcc---acaggagcatgctaatggtggaaaatgtattgtgtttactcaaactaaacgagagGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGCTTCATGGGGATATTTCACAGAATCAGAGAGAAAGGACACTATCAGGATTTC
                                                             |||| |   | | ||  | | |  |  |  || |   ||| |     || || |   |  | |  | || |    ||||||||||| || || |||||||| ||||| ||||| ||||| |||||||| || ||| |  |  |||||||  |||  || ||||    |||| | ||                                                     
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT---------------------------------------------------

upper sequence: LOC_Os07g05050.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------------------------------gtgagcactcttctgaatgtatgatgtgtt-ttatagtttgcaccgttaacgactcttttctct--acac----------ttccacaggagcatgctaatggtggaaaatgtattgtgtttactcaaactaaacgagagGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGCTTCATGGGGATATTTCACAGAATCAGAGAGAAAGGACACTATCAGGATTTC
                                                                                             |||  |   | |    | |||  |   |  || | | ||  |||   | | | | ||||| ||   |||          ||    |||| ||||| || ||||||||||||||||| || |||||||| ||||| || || ||| |||| |||||||||||||  || | ||    |||| |||| |                                                   
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC---------------------------------------------------
















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|29680607|gb|CB676882.1|CB676882
EST:     TTGCCTCTGAGCACTATGGGAAGCCATCAATTCTTGGTCCATTGATCAAA                         GCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGCTT
genomic: TTGCCTCTGAGCACTATGGGAAGCCATCAATTCTTGGTCCATTGATCAAAgtgagcactc ... taaacgagagGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaggagcatgctaatggtggaaaatgtattgtgtttactcaaactaaacgagagGCAGATAGATTAGCATATGCTATGGGCAGGAGCTATGCATGTCAGGCGCTTCATGGGGATATTTCACAGAATCAGAGAGAAAGGACACTATCAGGATTTC
                                          aactaaa  putative branch site (score: 2)
                     aaaatgtatt  TA-rich tract