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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactcatcgcagccagagttatagatcagctggtaaattttgttgtggtattgatgtttgtttatgagtcgcagGTCGAGATGGAGGGATGTAAAGCACCTATCACTACATTCATTGTGGAGCCTTTTGTGCCTCATGATCAAGAATACTACCTCTCTATAGTATCTGATAGAC

Basic information

species Arabidopsis thaliana
transcript AT1G09430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g47330.1 (Oryza sativa), 3'ss of exon 2
-------------gtgac--tcatcgcagccagagttata----gatcagctggtaaattttgttgtggtattgatgtttgtttatgagtcgcagGTCGAGATGGAGGGATGTAAAGCACCTATCACTACATTCATTGTGGAGCCTTTTGTGCCTCATGATCAAGAATACTACCTCTCTATAGTATCTGATAGAC
             |  |    | |   |  | || ||||     | ||   || ||||||  |||||  | |     | ||  |||      |||||||||||||  || || || || || ||||| || |||||||||||||| ||||| || |||||||||||||||||||| ||||| || || || || |
gtagttcaattttgctatcgcctttaaaatctgacttattctctgttcgcttgataaattaagttgttctgtcctattgtggctatt-----cagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCATTTGTACCCCATGATCAAGAATACTACCTTTCTATTGTCTCGGAGAGGC

upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 2
--------gtgactcat------cgcagccagagttatagatcagctggtaaattttgttgtg-gtattgatgtttgtttatgagtcgcagGTCGAGATGGAGGGATGTAAAGCACCTATCACTACATTCATTGTGGAGCCTTTTGTGCCTCATGATCAAGAATACTACCTCTCTATAGTATCTGATAGAC
        ||  ||  |         | || |   |  |||   |||     | ||  || || ||  ||   |   || ||   |  ||||| |||||||  || || || || || ||||| || ||||| || ||||| |||||||| ||||||||||| |||||||| || || || || || ||  
gtatagtagttgcttgtgtgaaaaataacctgtcctccagacatgctacatgagttgattttgtgtcatgtgatccattaatt--tttcagGTTGAGATGGGTGGCTGCAAGGCTCCAATCACGACCTTCATCGTCGAGCCATTTGTGCCACATGATCAAGAGTACTACCTTTCGATTGTCTCAGAGAGGT
















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|124912239|gb|EH986319.1|EH986319
EST:     TGGATCTTGCTGAAGTTGCAGACTTTGTCAAAGCCCGCCTCGGCACTGAG                         GTCGAGATGGAGGG
genomic: TGGATCTTGCTGAAGTTGCAGACTTTGTCAAAGCCCGCCTCGGCACTGAGgtgactcatc ... tgagtcgcagGTCGAGATGGAGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagatcagctggtaaattttgttgtggtattgatgtttgtttatgagtcgcagGTCGAGATGGAGGGATGTAAAGCACCTATCACTACATTCATTGTGGAGCCTTTTGTGCCTCATGATCAAGAATACTACCTCTCTATAGTATCTGATAGAC
                             tattgat  putative branch site (score: 3)
              taaattttgtt  TA-rich tract