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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttcacaatcttatgcttgatttcttgctaaaacagtattttgggtgttctattgatacaataacgcacttctgtgatcttcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC

Basic information

species Arabidopsis thaliana
transcript AT1G17370.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 5
-----------gttggttcacaatcttatgcttgatttcttgctaaaacagtattttgggtgttctattgatacaataacgcacttctgtgatcttcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC
             |||  |  |   | || || |   |  | ||     |   |||||| |    |||| |||  |||  ||   | |      || || ||||||||||| ||||||||||||||| ||| | ||||| |||||||||||||| | | ||||| | ||||| |||||||| || | ||| ||
aagcttaaacaaatgggccctatgttcatactaggcctgatcctttgggaac-ttttggctaagatatt-atattatatggcttgtttcc---tttaatttgcagGTCACTACAATATATTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGTTGTTTGCATGCTTTTCTGTCTATCCCAGTTGTTC

upper sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
------gttggttcaca-atcttatgcttgatttcttgctaaaacag---tattttgggtgttctattgatacaataacgcacttctgtgatcttcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC
       |  | | | | |  |    | |   ||| | ||||  | |      ||||||   | | | | ||   ||  ||  || | |    || || ||||||||| | ||| || |||||||| ||| | ||||| |||||||||||||| | ||||||| | ||||| |||||||| || ||||| ||
ataaaaataagcttaaacaaataggacctatgttcatactaagtctgatcccctttgggaacttt-tggctaaggtatagcctttttct---tttaatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC
















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|116486725|gb|EG529317.1|EG529317
EST:     TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA                         GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
genomic: TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAAgttggttcac ... tcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
EST: gi|116386087|gb|EG428679.1|EG428679
EST:     TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA                         GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
genomic: TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAAgttggttcac ... tcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
EST: gi|116486731|gb|EG529323.1|EG529323
EST:     TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA                         GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
genomic: TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAAgttggttcac ... tcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
EST: gi|124734324|gb|EH825726.1|EH825726
EST:     TTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA                         GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
genomic: TTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAAgttggttcac ... tcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
EST: gi|116486728|gb|EG529320.1|EG529320
EST:     TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA                         GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
genomic: TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAAgttggttcac ... tcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
EST: gi|116386137|gb|EG428729.1|EG428729
EST:     TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA                         GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
genomic: TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAAgttggttcac ... tcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
EST: gi|116477129|gb|EG519721.1|EG519721
EST:     TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA                         GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA
genomic: TATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAAgttggttcac ... tcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattttgggtgttctattgatacaataacgcacttctgtgatcttcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC
                       caataac  putative branch site (score: 2)
                                          tcttcat  putative PPT
               tattgatacaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttcacaatcttatgcttgatttcttgctaaaacagtattttgggtgttctattgatacaataacgcacttctgtgatcttcatgtgcagGTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT