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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctttgatcatgtttatttgttttcttatttttgtgccacccctcttatatttgagctgggaataacctaagacaagtcttgcttttttcgtactgggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGACTTGGCTTGGCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACT

Basic information

species Arabidopsis thaliana
transcript AT1G22300.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G22300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g05720.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------gtcctttgatcatgtttatttgttttcttatttttgtgccacccctcttatatttgagctgggaataacctaagacaagtcttgcttttttcg--tactgggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGACTTGGCTTGGCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACT
                                  |||   ||    ||  |  || | |||||||| |  | | ||| | || |||||  |  | |   |  ||     ||  |  ||   |    |  |     || |||||||      | | || |     | | || | || || |||||| | ||||||||  |||| ||||||||||| || ||||||||||| || |||||||
gtccttagcatctaattcctctgttgaagctcatcttacctctcactttgtcattgttttatttttttcaccctcctttaatttttgatttccgtagttcagaaacagggtgctagttcaattaattttttatgctgcagGCTGCCACCAGTACAGCTGCCTCAGATCTGCCGCCTACTCATCCAATCAGACTTGGGCTGGCTTTGAACTTTTCTGTCTTCTACTATGAAATTTTGAACT
















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|125125609|gb|EL171044.1|EL171044
EST:     AAGCATATAAG                         GCTGCTGTTGCTTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAG
genomic: AAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGC-TGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAG
EST: gi|124984411|gb|EL057069.1|EL057069
EST:     TGCAGATCAGTCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACA
genomic: TGCAGATCAGTCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACA
EST: gi|124962238|gb|EL036674.1|EL036674
EST:     TCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
genomic: TCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
EST: gi|125284521|gb|EL298606.1|EL298606
EST:     CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAAT
genomic: CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAAT
EST: gi|47830317|gb|CK120001.1|CK120001
EST:     CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
genomic: CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
EST: gi|124933497|gb|EL010649.1|EL010649
EST:     TCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
genomic: TCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
EST: gi|124727891|gb|EH819293.1|EH819293
EST:     CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAAT
genomic: CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAAT
EST: gi|47831981|gb|CK121665.1|CK121665
EST:     CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
genomic: CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
EST: gi|125233964|gb|EL248049.1|EL248049
EST:     TCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
genomic: TCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
EST: gi|47828961|gb|CK118645.1|CK118645
EST:     CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
genomic: CTGGTGCTGAACGCAAGGAAGCTGCAGATCAGTCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGA
EST: gi|125118909|gb|EL167387.1|EL167387
EST:     TGCAGATCAGTCTCTTGAAGCATATAAG                         GCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACA
genomic: TGCAGATCAGTCTCTTGAAGCATATAAGgtcctttgat ... gggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagctgggaataacctaagacaagtcttgcttttttcgtactgggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGACTTGGCTTGGCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACT
          gaataac  putative branch site (score: 2)
                                 tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctttgatcatgtttatttgttttcttatttttgtgccacccctcttatatttgagctgggaataacctaagacaagtcttgcttttttcgtactgggaatgtagGCTGCTGTTGCTGCTGCAGAGAATGGTTTGGCACCCACACATCCAGTTAGACTTGGCTTGGCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC