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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctctggaaagtttacatttttgggtggcttagttttgatgtctgggtttgattttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT

Basic information

species Arabidopsis thaliana
transcript AT3G23490.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g33270.1 (Oryza sativa), 3'ss of exon 1
-------------------gtttgctctggaaag-----tttaca----tttttgggtggcttagttttgatgtct----gggtttgattttg-atttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT
                     ||  | ||| ||      ||||||    | |      || ||  | ||||| | |       ||  || |||   | || ||||||||||| || ||||||||||| ||||| || ||||| ||||||||||| || ||||| ||||| ||
ttagtacacggttgatttaaattattgtggtaatgcacttttacaacactctagaaaaggattcttgttgatattttttttaattatatattgcgctcagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT

upper sequence: AT3G23490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G134747_T01 (Zea mays), 3'ss of exon 1
--------------------------------gtttgctctggaaagtttacatttttgggtggcttagtt-ttgatgtctgggtttgattttgatt-tagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT
                                ||||  || | |      | || || |  |  | |  || |  |  |      |  || ||| |   || ||||||||||| || ||||||||||| ||||| || ||||| || |||||||| || ||||| ||||| ||
gcttttatccagagctttgttagtttatttcagttta-tcagcactaacaagatattagaataacctttttgtcaacattgttactatatgttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT

upper sequence: AT3G23490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G134747_T02 (Zea mays), 3'ss of exon 1
--------------------------------gtttgctctggaaagtttacatttttgggtggcttagtt-ttgatgtctgggtttgattttgatt-tagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT----------------------------
                                ||||  || | |      | || || |  |  | |  || |  |  |      |  || ||| |   || ||||||||||| || ||||||||||| ||||| || ||||| || |||||||| || ||||| ||||| ||                            
gcttttatccagagctttgttagtttatttcagttta-tcagcactaacaagatattagaataacctttttgtcaacattgttactatatgttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATGTAAGAGATACCAGTGCTTCATTTATGC

upper sequence: AT3G23490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G00790.1 (Glycine max), 3'ss of exon 1
------------------------------gtttgctctggaaagtttacatttttgggtggcttagttttgatgtctgggtttgattttgattt---agGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT
                              || |  |    |     | | ||||        ||| |||    |  |  | |    ||  ||||   |||||||||||||| || ||||||||||| ||||| || || || || |||||||| || ||||| ||||| ||
ttgaggattctaatgttggaaatatgtcaagtgtaatgcatatcaacttccttttatatatatttaatttgttgggttatgctgatcttctatttcatagGTTGAATGAAGCTGTTATGCATTTTGGGGAGAGCATCAAAGAAATAATCAATGAGGAGTTTGGTGATGGGAT

upper sequence: AT3G23490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0049g01520.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------gtttgctctggaaagtttacatttt-tgggtggcttagttttgatgtctgggttt--gattttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT
                                  |  ||     ||  | |  ||||| ||  |||| |  ||    |  |||  |||   | |||||   || ||||||||||| |||||||||||||||||||| || ||||| ||||||||||| || ||||| ||||||||
cagaagcaatttgtcatctaagtaaggttttgcataagcatacaaatctctgaattttctgactggcgtgtttccatttgctgactttccaactttga---agATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT

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|125285556|gb|EL299641.1|EL299641
EST:     AGATCCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAG                         GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATC
genomic: AGATCCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAGgtttgctctg ... tttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATC
EST: gi|125306193|gb|EL320278.1|EL320278
EST:     ATCCTAATCTCATCCAAGAACCCACTATCTACAG                         GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
genomic: ATCCTAATCTCATCCAAGAACCCACTATCTACAGgtttgctctg ... tttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
EST: gi|86077490|gb|DR373247.1|DR373247
EST:     CCGTGGAGATCCTACGATCCTAATCTCATCCAAGAACCCACTATCTACAG                         GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
genomic: CCGTGGAGATCCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAGgtttgctctg ... tttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
EST: gi|164119666|gb|ES014784.1|ES014784
EST:     CCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAG                         GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
genomic: CCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAGgtttgctctg ... tttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
EST: gi|116453344|gb|EG495936.1|EG495936
EST:     CCGTGGAGATCCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAG                         GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
genomic: CCGTGGAGATCCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAGgtttgctctg ... tttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
EST: gi|124707805|gb|EH799207.1|EH799207
EST:     TCCAAGAACCCACTATCTACAG                         GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
genomic: TCCAAGAACCCACTATCTACAGgtttgctctg ... tttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
EST: gi|125078817|gb|EL141056.1|EL141056
EST:     CCGTGGAGATCCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAG                         GTTGAATGAAGCAGTGATGCATTTTGGTGAGA
genomic: CCGTGGAGATCCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAGgtttgctctg ... tttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGA
EST: gi|116453343|gb|EG495935.1|EG495935
EST:     CCGTGGAGATCCTATGATCCTAATTTCATCCAAGAACCCACTATTTACAG                         GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
genomic: CCGTGGAGATCCTATGATCCTAATCTCATCCAAGAACCCACTATCTACAGgtttgctctg ... tttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
EST: gi|125271932|gb|EL286017.1|EL286017
EST:     GAACCCACTATCTACAG                         GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA
genomic: GAACCCACTATCTACAGgtttgctctg ... tttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttacatttttgggtggcttagttttgatgtctgggtttgattttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT
                                            ttttgat  putative branch site (score: 4)
                                       tttgattttgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctctggaaagtttacatttttgggtggcttagttttgatgtctgggtttgattttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG