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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcaattggttcaactaagagtctggtgaattgtctatggagtgattatatgtgtactctgatagataaggatttgcattctgagatttgcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA

Basic information

species Arabidopsis thaliana
transcript AT4G15930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G472231_T01 (Zea mays), 3'ss of exon 1
----------------------------------aatcaattggttcaactaagagtctggtgaattgtctatggagtgattatatgt--------gtactctgatagataaggatttgcattctgagatttgcttttgc----agGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA
                                    |   |  | || | |  |  || |  |       | | ||  | || |  ||        | | |  |  |  |  ||| ||   |   ||    | || |  |    |||| || |||||| ||||| |||||||||| || || ||| | |||||||||||||| |||||||| || ||  | || ||||| ||||| || || ||||
gtaagaaccttatgcccttgctctcgctctgccttcttcctgcgctcgatttggtttccgtcgctccccttgttgaccggttcttcgttgggaatgggatttggccatttggggacttttctgtcgattccttctctgtcggtcagGCATTCGAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCA

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G146012_T01 (Zea mays), 3'ss of exon 1
-----aatcaattggttcaactaagagtct-------ggtgaattgtctatggagtgattatatgtgtactctgatagataaggatttgcattctgagatttgcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA
     || |  | | |    ||  |  |         | |  |||  |  | |  |||     |||    | | ||   ||||  |||   |||||    |||||| | |||||||| || ||| ||||  |||||||||| || |||||| | |||||||||||||| |||||||| || ||  | || ||||| ||||| || || ||||
gtaagaacctctcgctctcgctctgccttcttcatgcgatcgattcccccttgt-tgacgggttgttcgttataattt-taagatttttttttctgtcgattgcttct-cagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCA

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G16050.1 (Glycine max), 3'ss of exon 1
--------------------aatcaattggttcaactaagagtctggtgaattgtctatggagt-gattatatgtg-tactctgatagataaggatttg--cattctgagatttgcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA
                      |   ||  |     |    || | |     ||| | |||  | | || |   || | |  ||    |||| |  |||  |||| || |  ||  |    ||||||||||||||||||| ||||||||| ||| | || ||| | |||||||||||||| || ||||  |||||  | |||||||||||||| |||||||| |
gttagtttcgacaactttctcctttttttttgtggttcctcgttttggattctgtttctgggtttggttgtgcttgctgcgttgtgtcataaagtcttgaccattttgcggattatt----cagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G04830.1 (Glycine max), 3'ss of exon 1
--------------------aatcaattggtt-caactaagagtctggtgaattgtctatggagt-gattatatgtg-tactctgatagataaggatttgcattctgagatttgcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA
                      ||  ||  ||     |    || | |     ||| | |||  | | || |   || | |  ||     ||| |  |||   | |  |    | || | ||||||||||||||||||| ||||||||| ||  | || ||| | |||||||||||||| || ||||  |||||  | |||||||||||||| |||||||| |
gttagtctcaacaactttcttctcttttttttatggttcttcgttttggattctgtttctgggtttggttgtgcttgctgcgttgtgtcgtaaagtcttgacctttttg--cggattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTA

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G04820.1 (Glycine max), 3'ss of exon 1
-------------------------------aatcaattggttcaactaagagtctggtgaattgtctatggagt-gattatatgtg-tactctgatagataaggatttg--cattctgagatttgcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA
                                 ||  ||  |     |    || | |     ||| | |||  | | || ||  || |    ||     ||| |  |||  | || || |  ||| |    ||||||||||||||||||| ||||||||| ||  | || ||| | |||||||||||||| || ||||  |||||  | || |||||||| || ||||| || |
gttagttttaacgactctctctctctatatctctctctttttatggttcctcgttttggattctgtttctgggtttggttgtacttgctgtgttgtgtcgtaaagtcttgacctttttgcggattgtt----cagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACGTGGCATTGTATCGTTGGACGTA

upper sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
----------------aatcaattggttcaactaagagtctggtgaattgtcta-tggagtga--ttatatgtgtactctgatagata---aggatttgcattctgagatttgcttttg--cagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA
                  ||||||  ||   || ||  | |  |   |||   | ||||   |  |||  | | |  |||| | |||      |||||         | | || | |    ||||| |  |||||  |||||||||||||  | || || ||| |||| ||||||||||| || ||||| |||||  |||| |||||||||||||| |||||||
gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataatttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA

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|163989178|gb|ES145125.1|ES145125
EST:     CAAAAGGAAGCTATCGAAATCGCCATCTCC                         GCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
genomic: CAAAAGGAAGCTATCGAAATCGCCATCTCCgttagtctct ... gcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
EST: gi|86074680|gb|DR370437.1|DR370437
EST:     CCGATATGAAAGATGATATGCAAAAGGAAGCTATCGAAATCGCCATCTCC                         GCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
genomic: CCGATATGAAAGATGATATGCAAAAGGAAGCTATCGAAATCGCCATCTCCgttagtctct ... gcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
EST: gi|86081177|gb|DR376934.1|DR376934
EST:     CCGATATGAAAGATGATATGCAAAAGGAAGCTATCGAAATCGCCATCTCC                         GCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
genomic: CCGATATGAAAGATGATATGCAAAAGGAAGCTATCGAAATCGCCATCTCCgttagtctct ... gcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
EST: gi|19741173|gb|AU226526.1|AU226526
EST:     GAAAGATGATATGCAAAA-GAAGCTATCCAAATCGCCATCTCC                         GCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
genomic: GAAAGATGATATGCAAAAGGAAGCTATCGAAATCGCCATCTCCgttagtctct ... gcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
EST: gi|164033193|gb|ES109245.1|ES109245
EST:     CCGATATGAAAGATGATATGCAAAAGGAAGCTATCGAAATCGCCATCTCC                         GCGTTTGAGAAGTACAGTGTG
genomic: CCGATATGAAAGATGATATGCAAAAGGAAGCTATCGAAATCGCCATCTCCgttagtctct ... gcttttgcagGCGTTTGAGAAGTACAGTGTG
EST: gi|124935753|gb|EL012713.1|EL012713
EST:     AAGCTATCGAAATCGCCATCTCC                         GCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
genomic: AAGCTATCGAAATCGCCATCTCCgttagtctct ... gcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAG
EST: gi|125306589|gb|EL320674.1|EL320674
EST:     TATGAAAGATGATATGCAAAAGGAAGCTATCGAAATCGCCATCTCC                         GCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAA
genomic: TATGAAAGATGATATGCAAAAGGAAGCTATCGAAATCGCCATCTCCgttagtctct ... gcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatatgtgtactctgatagataaggatttgcattctgagatttgcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA
            ctctgat  putative branch site (score: 4)
                                          tttgctttt  putative PPT
                 atagataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcaattggttcaactaagagtctggtgaattgtctatggagtgattatatgtgtactctgatagataaggatttgcattctgagatttgcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
aatcaat
- - - - - - caactaa