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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttccgtattcgtatatgctttagcgcatttacattctcattgttatttgttaatactagcactattcatgtgtgatgttttcttttgtgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATCGTCCTCCCTCTACCTGG

Basic information

species Arabidopsis thaliana
transcript AT3G04820.1
intron # 14
splice site 3'
intron type U2

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|116457912|gb|EG500504.1|EG500504
EST:     ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAG                         GTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
genomic: ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAGgttagttttt ... tgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
EST: gi|116457905|gb|EG500497.1|EG500497
EST:     ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAG                         GTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
genomic: ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAGgttagttttt ... tgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
EST: gi|116457913|gb|EG500505.1|EG500505
EST:     ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAG                         GTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
genomic: ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAGgttagttttt ... tgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
EST: gi|116457903|gb|EG500495.1|EG500495
EST:     ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAG                         GTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
genomic: ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAGgttagttttt ... tgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
EST: gi|116457908|gb|EG500500.1|EG500500
EST:     ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAG                         GTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
genomic: ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAGgttagttttt ... tgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
EST: gi|116457916|gb|EG500508.1|EG500508
EST:     ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAG                         GTTGTAAGTATAGAGGATTTGGAAGCTGGAACCTACTCGACCAGTGACATC
genomic: ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAGgttagttttt ... tgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
EST: gi|116457919|gb|EG500511.1|EG500511
EST:     ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAG                         GTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
genomic: ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAGgttagttttt ... tgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATC
EST: gi|116457901|gb|EG500493.1|EG500493
EST:     ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAG                         GTTGTAAGTATAGAGGATTTGGAAGCTGGAACT
genomic: ATGATACTGCTGTTGTAGATCTTCCAGCTGAAAGGAGTGACCTTGTTAAGgttagttttt ... tgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttgttaatactagcactattcatgtgtgatgttttcttttgtgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATCGTCCTCCCTCTACCTGG
     tgttaat  putative branch site (score: 3)
                                   ttttcttttgtgttct  putative PPT
       ttaatacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttccgtattcgtatatgctttagcgcatttacattctcattgttatttgttaatactagcactattcatgtgtgatgttttcttttgtgttcttcagGTTGTAAGTATAGAGGATTTGGAAGCTGGAACTTACTCGACCAGTGACATCGTCCTCCCTCTACCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA