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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagatctgatttttgcatataagattcgagaagaaggaatttggttgattaagctgagaaagttctgatttttcagGAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTTAATAAAGTTGAAGACTTTAGCAATT

Basic information

species Arabidopsis thaliana
transcript AT2G39670.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g01070.t01 (Vitis vinifera), 3'ss of exon 1
-----------------gtaaagatctgatttttgcat--ataagat-tcgagaagaaggaatttggttgattaagctgagaaagttctgattt-ttcagGAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTTAATAAAGTTGAAGACTTTAGCAATT
                  | |    |  |   | ||||  |||  || | |  ||       ||||| || | ||  ||  |   | ||  | | ||||| || | || || || |||||||||||||||||||| |||||||||||||| ||  || || || | || ||  | |
tgcgtttcctatactttctcagccaccaaacatggcatgaatagcatattggtaatgcattttttgggtgttcaatttgtaattttgctattgtgttcagCAAAGCTATAGGGGGAAGCAGCTCCATCATCTTATCTACAAGAGAAAGGTCAAAGAAATTCAACATTTCAGTCAAT
















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|125053480|gb|EL124550.1|EL124550
EST:     TCGGAATGTCGGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAA                         GAAGGATACAGAGGAAAGCAGCTCCATCAT
genomic: TCGGAATGTCAGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAAgtaaagatct ... gatttttcagGAAGGATACAGAGGAAAGCAGCTCCATCAT
EST: gi|86070407|gb|DR366164.1|DR366164
EST:     TCGGAATGTCAGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAA                         GAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTT
genomic: TCGGAATGTCAGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAAgtaaagatct ... gatttttcagGAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTT
EST: gi|86070406|gb|DR366163.1|DR366163
EST:     TCGGAATGNCAGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAA                         GAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTT
genomic: TCGGAATGTCAGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAAgtaaagatct ... gatttttcagGAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTT
EST: gi|86070408|gb|DR366165.1|DR366165
EST:     TCGGAATGTCAGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAA                         GAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTT
genomic: TCGGAATGTCAGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAAgtaaagatct ... gatttttcagGAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTT
EST: gi|86070405|gb|DR366162.1|DR366162
EST:     TCGGAATGTCAGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAA                         GAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTT
genomic: TCGGAATGTCAGAGCCTGAGCTTCAAGAGCTTGCTATCAACCTCGGTCAAgtaaagatct ... gatttttcagGAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattcgagaagaaggaatttggttgattaagctgagaaagttctgatttttcagGAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTTAATAAAGTTGAAGACTTTAGCAATT
                                         ttctgat  putative branch site (score: 3)
                                               tttttc  CT-rich tract
                       ttgattaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagatctgatttttgcatataagattcgagaagaaggaatttggttgattaagctgagaaagttctgatttttcagGAAGGATACAGAGGAAAGCAGCTCCATCATCTTATTTACAAGAGAAAGGTTAATAAAGTTGAAGACTTTAGCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA