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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaataatcggatgcagtaaatgcttgccatctctattccaccttgtagttgatcaaaatagtttaatgtctatactaatatgtgaggtggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATCATTTCCACTACTATTGGAGGCAAAAACGGCGAACCAAAGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G06390.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 1
-ttgaaataatcggatg-cagtaaatgcttgccatctctattccaccttgt---agttgatcaaaatagtttaatgtctatactaatatgtgaggtggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATCATTTCCACTACTATTGGAGGCAAAAACGGCGAACCAAAGCAG
 |   | | ||    |  || ||||    || |||    || |    ||     | ||| |  |     || ||| |||||     | | | |      |||||||| ||||| ||  |||| |||||||| ||||| || |||||||| || || || ||||| || |||||||||||||| || ||||| || |||
ttatgattgatattgtatcaataaaaatctgacattcgaatactgtattaggagatttgctttactgcattaaatatctatttctttttataat-----ttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 1
-ttgaaataatcggatg-cagtaaatgcttgccatctctattccaccttgtagttgatcaaaatagtttaatgtctatactaatatgtgaggtggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATCATTTCCACTACTATTGGAGGCAAAAACGGCGAACCAAAGCAG
 |   | | ||    |  || ||||    || |||     | |    ||   |    |     || |  | |   ||| |||||   ||   |   |||||||| ||||| ||  |||| |||||||| ||||| ||||| ||||| || || || ||||| || |||||||||||||| || ||||| ||  ||
atatgattgatattgtatcaataaaaatctgacattcaagtactgtatta-ggagatttgctttactgcattaaatat-ctaattcttgttataagttgcagGATATGTCAGCTACTGTCATTGAGGGGAATGATGCTGTCACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAAGAG

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 1
--ttgaaataatcggatgcagtaaatgcttgccatctctattccaccttgtagttgatcaaaatagtttaatgtctatactaatatgtgaggtggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATCATTTCCACTACTATTGGAGGCAAAAACGGCGAACCAAAGCAG
  | ||||||   |   ||| ||   |      ||| |||||  || |  | |      |   |   || || |   | |||  |  ||| ||| ||||||||||||||| || |||||||||||||| |||||  | || ||||||||||| |||||||| || |||||||||||||| || || || || |||
tttagaaatagcagctagcaatagg-gaagattatc-ctatttgacataattggcatgtattttgcatttattttattcctatgacttgatgtgaattgcagGAAATGTCAGCTGCTGTTATTGAGGGGAATGATCCAGTCACTGGTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG

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|86037640|gb|DR333395.1|DR333395
EST:     TCACGACGGCGACGGSTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TCACGACGGCGAC-GCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037629|gb|DR333384.1|DR333384
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037635|gb|DR333390.1|DR333390
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037634|gb|DR333389.1|DR333389
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037637|gb|DR333392.1|DR333392
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGVTAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037633|gb|DR333388.1|DR333388
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037631|gb|DR333386.1|DR333386
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037632|gb|DR333387.1|DR333387
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037630|gb|DR333385.1|DR333385
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037641|gb|DR333396.1|DR333396
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037638|gb|DR333393.1|DR333393
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037636|gb|DR333391.1|DR333391
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATC
EST: gi|86037639|gb|DR333394.1|DR333394
EST:     TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAG                         GAAATGTCTGCAGCTGTTATTGAGGGAAA
genomic: TTCACGACGGCGACGCTTTGAAACGCCGTCCTGAATTGGATTCTGATAAGgtttatttct ... tggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagttgatcaaaatagtttaatgtctatactaatatgtgaggtggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATCATTTCCACTACTATTGGAGGCAAAAACGGCGAACCAAAGCAG
                              tactaat  putative branch site (score: 1)
            aaaatagtttaatgtc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaataatcggatgcagtaaatgcttgccatctctattccaccttgtagttgatcaaaatagtttaatgtctatactaatatgtgaggtggattgcagGAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATCATTTCCACTACTATTGGAGGCAAAAACGGCGAACCAAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- gaaataa
- - - - - - - - - - - - - - - catctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaaa