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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgtccatttttatatatacttttttggtcacttgtgataattatctgaagttgttgaggttatttttattgttttgattgacaatttggatttctttataattatttttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGACTGATTCTGTGCAAAGCAGATCTTCAGGACTACGAGGCTCTTAAGGCGGC

Basic information

species Arabidopsis thaliana
transcript AT1G15950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G15950.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0070g00240.t01 (Vitis vinifera), 3'ss of exon 1
gtacttgtccatttttatatatacttttttggtcacttgtgataattatctgaagttgttgaggt-tattttta----ttgt----tttgattgacaat-ttggatttctttataattatttttct-----tgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGACTGATTCTGTGCAAAGCAGATCTTCAGGACTACGAGGCTCTTAAGGCGGC
||   |   ||  | |  || |  ||| | |    ||   |     | | ||   |||  ||||  ||  | |     |||     |||   | |||||  |   ||| ||||   |||||||| |     | |||||||||| |||||  | ||||||||||| || ||||||| |||||||||| ||||| | |||||||| ||||||  ||| || |||  ||| || | |||
gtgggtagacacatgtg-atgtgatttctagtgagctaaggtctcatttgtggcattgaagaggcatacctctgaggcttgcgccatttctgtaacaatactctttttttttaattttatttttatgggattacagATGATCCAAAGAATTCTCATTTGAGAGAGCTTGAAGGAGCAAAGGAGAGATTGATTTTATGCAAAGCTGATCTTATGGATTATGAGAGTCTGAAAGAGGC
















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|116464127|gb|EG506719.1|EG506719
EST:     GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAG                         ATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
genomic: GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAGgtacttgtcc ... tttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
EST: gi|47829558|gb|CK119242.1|CK119242
EST:     GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAG                         ATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
genomic: GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAGgtacttgtcc ... tttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
EST: gi|125058370|gb|EL127189.1|EL127189
EST:     CACAGTCAAAGGAACCGTACGGAATCCAG                         ATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAG
genomic: CACAGTCAAAGGAACCGTACGGAATCCAGgtacttgtcc ... tttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAG
EST: gi|19875544|gb|AU236375.1|AU236375
EST:     GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAG                         ATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
genomic: GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAGgtacttgtcc ... tttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
EST: gi|125192349|gb|EL207303.1|EL207303
EST:     ACCGTACGGAATCCAG                         ATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAG-AGAGAC
genomic: ACCGTACGGAATCCAGgtacttgtcc ... tttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
EST: gi|116438546|gb|EG481138.1|EG481138
EST:     GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAG                         ATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
genomic: GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAGgtacttgtcc ... tttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
EST: gi|116464136|gb|EG506728.1|EG506728
EST:     GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAG                         ATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
genomic: GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAGgtacttgtcc ... tttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
EST: gi|116438547|gb|EG481139.1|EG481139
EST:     GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAG                         ATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC
genomic: GATACTTCTCGAGAGAGGTTACACAGTCAAAGGAACCGTACGGAATCCAGgtacttgtcc ... tttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttattgttttgattgacaatttggatttctttataattatttttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGACTGATTCTGTGCAAAGCAGATCTTCAGGACTACGAGGCTCTTAAGGCGGC
              gattgac  putative branch site (score: 3)
                                        ttatttttctt  putative PPT
                     aatttggatttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgtccatttttatatatacttttttggtcacttgtgataattatctgaagttgttgaggttatttttattgttttgattgacaatttggatttctttataattatttttcttgcagATGATCCGAAGAACACACATTTGAGAGAACTAGAAGGAGGAAAGGAGAGACTGATTCTGTGCAAAGCAGATCTTCAGGACTACGAGGCTCTTAAGGCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT