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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAAGCTCTCATAGAGTATGATGCCATGGTTTGGACAGATCAAGTTATTGATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAGgtaaatgaatgtcttctttgaagctctttttgacattccacaaggaagtctgaaacaagttcttccacttctttacag

Basic information

species Arabidopsis thaliana
transcript AT4G36530.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G36530.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA16G25200.2 (Glycine max), 5'ss of exon 4
ACAAAGCTCTCATAGAGTATGATGCCATGGTTTGGACAGATCAAGTTATTGATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAGgtaaatgaatgtcttctttgaagct-ctttttgacattccacaaggaagtctgaaacaagttc-ttccactt-ctttacag--------------------
||||||| || ||||| |||||||| ||||| |||| |||||||||| |||| ||  |||| ||  |||| ||||||||| | ||| | |||||||||||||||   | | |  |   ||||  | | |   |  |||   |    | | | ||  |   ||| ||||||    ||||  |                    
ACAAAGCACTTATAGATTATGATGCTATGGTGTGGAGAGATCAAGTTGTTGACTTTGTGAAGGAAATAGTAAAAGAACCAACCGTTTTAGTTGGAAACAGgtaag-aactatactacctgaatttacatcagggaattaggctgaaatgccagattcttcttcattccacaagttttagtgtttgctttccctgcatggtt
















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|125010335|gb|EL082604.1|EL082604
EST:     GATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAG                         CCTTGGGGGATTTACGGCATTGTCAGTTGCGGTTGGATTACCC
genomic: GATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAGgtaaatgaat ... ttctttacagCCTTGGGGGATTTACGGCATTGTCAGTTGCGGTTGGATTACCC
EST: gi|125211016|gb|EL225970.1|EL225970
EST:     GATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAG                         CCTTGGGGGATTTACGGCATTGTCAGTTG
genomic: GATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAGgtaaatgaat ... ttctttacagCCTTGGGGGATTTACGGCATTGTCAGTTG
EST: gi|125117860|gb|EL166816.1|EL166816
EST:     GCTGTTGTCGTTGGAAACAG                         CCTTGGGGGATTTACGGCATTGTCAGTTGCGGTTGGATTACCCGAGCAAGT
genomic: GCTGTTGTCGTTGGAAACAGgtaaatgaat ... ttctttacagCCTTGGGGGATTTACGGCATTGTCAGTTGCGGTTGGATTACCCGAGCAAGT
EST: gi|125009045|gb|EL081314.1|EL081314
EST:     GATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAG                         CCTTGGGG-ATTTACGGCATTGTCAGTTGCGGTTGGATTACCC
genomic: GATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAGgtaaatgaat ... ttctttacagCCTTGGGGGATTTACGGCATTGTCAGTTGCGGTTGGATTACCC
EST: gi|124867146|gb|EH951583.1|EH951583
EST:     TTTCATGAAAGAGGTAGTGAAAGAACCAGCTTGTTGTCGTTGGAAACAG                         CCTTGGGGGATTTACGGCATTGTTCAGTTGCGGTTGGATTACCCGAGCAAG
genomic: TTTCATGAAAGAGGTAGTGAAAGAACCAGC-TGTTGTCGTTGGAAACAGgtaaatgaat ... ttctttacagCCTTGGGGGATTTACGGCATTG-TCAGTTGCGGTTGGATTACCCGAGCAAG
EST: gi|124754444|gb|EH844574.1|EH844574
EST:     GTGAAAGAACCAGCTGTTGTCGTTGGAAACAG                         CCTTGGGGGATTTACGGCATTGTCAGTTGCGGTTGGATTACCCGAGCAAG
genomic: GTGAAAGAACCAGCTGTTGTCGTTGGAAACAGgtaaatgaat ... ttctttacagCCTTGGGGGATTTACGGCATTGTCAGTTGCGGTTGGATTACCCGAGCAAG
EST: gi|124902283|gb|EH976363.1|EH976363
EST:     GATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAG                         CCTTGGGGGATTTACGGCATTGTCAGTTGCGGTTGG
genomic: GATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAGgtaaatgaat ... ttctttacagCCTTGGGGGATTTACGGCATTGTCAGTTGCGGTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAAGCTCTCATAGAGTATGATGCCATGGTTTGGACAGATCAAGTTATTGATTTCATGAAAGAGGTAGTGAAAGAACCAGCTGTTGTCGTTGGAAACAGgtaaatgaatgtcttctttgaagctctttttgacattccacaaggaagtctgaaacaagttcttccacttctttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT