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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctcttttctaaaatatgaccattgttggagaagtggcctaagattctcttgcatacttgatctctttagtagattctttctgttggggttcgttcctagttgatgataatttgttttgaacctttgaacaattgcagCAAATGTTGAAGTACAATCCAGCAGAAAGAATTTCAGCAAAAGCAGCTCTCGATCATCCCTACTTTGACAGCCTTGACAAATCTCAGTTCTGACCTCTGC

Basic information

species Arabidopsis thaliana
transcript AT2G38620.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38620.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G495626_T03 (Zea mays), 3'ss of exon 6
gtaatgctcttttctaaaatatgaccattgttggagaagtggcctaagattctcttgcatacttgatctctttagtagattctttctgttggggttcgttcctagttgatgataatttgttttgaacctttgaacaattgcagCAAATGTTGAAGTACAATCCAGCAGAAAGAATTTCAGCAAAAGCAGCTCTCGATCATCCCTACTTTGACAGCCTTGACAAATCTCAGTTCTGACCTCTGC
                              |||||    ||    |  || |  ||| | |    |  |      |   || |||||      |   |    |   || ||| ||||||| || |   | ||     |||||| ||||| |  ||    ||||  || | || || |||||   ||| ||  | || |||||||||||| ||||||||||||| || |||||||  ||  || 
-----------------------------tttgga----tgtttcaccatccctttgaacaaaaaaaataagctatgttttgtttctaaaaaagaaagaaattg--tgctgacaatttgtattca---tgtg-----ttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATGGAGCATCCCTACTTTAACAGCCTTGACAAGTCCCAGTTCTAGCCGTTGT

upper sequence: AT2G38620.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G02400.1 (Glycine max), 3'ss of exon 3
gtaatgctcttttctaaaatatgaccattgttggagaa-gtggcctaagattctcttgcatacttgatctctttagtagattctttctgttggggttcgttcctagttgatgataatttgttttgaacctttgaacaattgcagCAAATGTTGAAGTACAATCCAGCAGAAAGAATTTCAGCAAAAGCAGCTCTCGATCATCCCTACTTTGACAGCCTTGACAAATCTCAGTTCTGACCTCTGC
                             | |||||   ||  | ||| ||  |     |      ||  |||   || || ||   |         | ||||  |||    | ||         ||  |||   ||  ||||| ||||| | ||||| |||||  | || ||||| || || || ||||| || |||||||| ||||||||||| |||||||||||||| || |        |
-----------------------------gctggagcttgttacataatataataccatacttcaaataacttccatacatgctacattca------ctttccccgttttcaacaaaa------aaaatttt---cacctgcagAAAATGCTCAAGTATAATCCTTCTGAGAGAATATCTGCTAAGGCAGCACTTGATCATCCATACTTTGACAGTCTTGACAAATCTCAATTTTAGTTGAGCC

upper sequence: AT2G38620.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0056g00210.t01 (Vitis vinifera), 3'ss of exon 4
gtaatgctcttttctaaaatatgaccattgttggagaagtggcctaagattctcttgcatact-tgatctctttagtagattctttctgttggggttcgttcctagttgatgataatttgttttgaacctttgaacaattgcagCAAATGTTGAAGTACAATCCAGCAGAAAGAATTTCAGCAAAAGCAGCTCTCGATCATCCCTACTTTGACAGCCTTGACAAATCTCAGTTCTGACCTCTGC
                                 || ||    |   ||   ||  ||| |||  |  | |  || ||  ||   || || ||   || |  |  | || |   ||  || || ||    |||| | | |||||| | ||| | || ||  | ||| | |||||||| ||||| ||||||||| | |||||||||||||| |||||||||||||||||||| ||||||  |    
--------------------------------tgacaatcaac---agtccctgctgcctacagtagtgttatttgtctat--attttgctgaaatttg--cgaatttaacagtacatttttgtg----tttggata-ttgcagAAGATGCTTAAATATGACCCATCTGAAAGAATCTCAGCTAAAGCAGCTTTGGATCATCCCTACTTCGACAGCCTTGACAAATCTCAATTCTGAAGTTGTT

upper sequence: AT2G38620.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S61_200V6.1 (Physcomitrella patens), 3'ss of exon 7
----------gtaatgctctt---ttctaaaatatg-accattgttggagaagtggcctaagattctcttgcatacttgatctctttagtagattctttctgttggggttcgttcctagttgatgataatttgttttgaacctttgaacaattgcagCAAATGTTGAAGTACAATCCAGCAGAAAGAATTTCAGCAAAAGCAGCTCTCGATCATCCCTACTTTGACAGCCTTGACAAATCTCAGTTCTGACC-TCTGC
             |||| | |     ||   || || |   ||| | |  ||    | | | ||| | |   ||| ||| |||   | | |  |     ||         | ||| | |||  ||   | |  |  |  |  |||  |   |||||||   ||||| | ||||| |||||  |  |||||||||| || | |||||| |  || ||||| |||||||||||||||||||| ||||| |||   | || 
gtaagtatccaccatgcacgtggcccctgtgatgtggaatcttgcttggaaacgaacattaaattattt---atagttggtcttgcttgcaagtagaaactaagttctacccttctttgtttctgtacactcatggtataggttttgat--ttgcagCGCTTGTTGCAATACAACCCAGCGAATCGAATTTCAGCTAAGGAAGCTCTAGTCCACCCCTATTTTGACAGCCTTGACAAATCACAGTTTTGAGTGTTTG-

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|86066648|gb|DR362405.1|DR362405
EST:     ATCACGTGCTGTTCCATCTCTATCTCCTGGAAGGAAT-GATCTTCTCACG                         CAAATGTTGAAGTACAATCCAGC
genomic: ATCACGTGCTGTTCCATCTCTATCTCCTG-AAGGAATTGATCTTCTCACGgtaatgctct ... acaattgcagCAAATGTTGAAGTACAATCCAGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggggttcgttcctagttgatgataatttgttttgaacctttgaacaattgcagCAAATGTTGAAGTACAATCCAGCAGAAAGAATTTCAGCAAAAGCAGCTCTCGATCATCCCTACTTTGACAGCCTTGACAAATCTCAGTTCTGACCTCTGC
               agttgat  putative branch site (score: 5)
                    atgataatttgtttt  TA-rich tract