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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaatggacatgattattagcctttgggcattttagcatgaacaagatactctgttttccaagttttggattacattgtttactctaatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA

Basic information

species Arabidopsis thaliana
transcript AT1G17370.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
gtaagttaatggacatgattattagcctttgggcattttagcatgaacaagatactctgttttccaagttttggattacattgtttactctaatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA
               | | | ||   |||| |   || |   |     |    | | ||| ||| || |||   | | || || ||         ||||| |||||||| |||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||| 
--------------gtaagtgttgctctttagat-ttatgttaaattgatttcattttgtattctaatttt---aattcaatgctt---------tgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttaatggacatgattattagcctttgggcattttagcatgaacaagatactctgttttccaagttttggattacattgtttactctaatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA
               | |  |  | || |||   |||||    |     | ||  |  | |||    ||||  | || | |  |||  | |||| |||||||||||||| |||||||| ||||| ||||| ||||| ||||| || |||||||| |||||| 
--------------gtaag-aagaacccttg---atttttatttatgttacatgttgggattt----gtttctg-ttgc-tcattt--tgtaatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S84_51V6.1 (Physcomitrella patens), 3'ss of exon 4
-----gtaagttaatg-gacatgattattagcctttgggcattttagcatgaacaagatactctgttttccaagttttggattacattgtttactctaatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA
     | || |   |   | | ||| |   | |      |   ||   ||| |      | |  | |  |    || |  | |||  ||   |  || || ||||||||||||||| ||||||| || || ||||| |||||||| || || || ||||||||| || 
tggtcgcaaatagttttaaaacgataaaacgacgaaatccgaattcttatggattttgaaattggctggc---attctcaaatactctg---aggctgatttgcagGTTTGGGCAATCTATCAAAGTAAATTGGGCATATGCGAGCGGACAAAGAGAGGATACAACAG

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:     GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTT                         GTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
genomic: GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTTgtaagttaat ... taatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
EST: gi|116386087|gb|EG428679.1|EG428679
EST:     GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTT                         GTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
genomic: GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTTgtaagttaat ... taatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
EST: gi|116486731|gb|EG529323.1|EG529323
EST:     GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTT                         GTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
genomic: GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTTgtaagttaat ... taatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
EST: gi|125050686|gb|EL122955.1|EL122955
EST:     GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTT                         GTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGG
genomic: GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTTgtaagttaat ... taatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGG
EST: gi|116486728|gb|EG529320.1|EG529320
EST:     GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTT                         GTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
genomic: GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTTgtaagttaat ... taatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
EST: gi|124883815|gb|EH962717.1|EH962717
EST:     TGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTT                         GTTTGGGCAACCTATCAAG
genomic: TGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTTgtaagttaat ... taatgtgcagGTTTGGGCAACCTATCAAG
EST: gi|116386137|gb|EG428729.1|EG428729
EST:     GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTT                         GTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
genomic: GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTTgtaagttaat ... taatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
EST: gi|116477129|gb|EG519721.1|EG519721
EST:     GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTT                         GTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
genomic: GATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTTgtaagttaat ... taatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGA
EST: gi|125049684|gb|EL121953.1|EL121953
EST:     AATGGAAGGCATTT                         GTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGG
genomic: AATGGAAGGCATTTgtaagttaat ... taatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaagatactctgttttccaagttttggattacattgtttactctaatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA
                                          ctctaat  putative branch site (score: 3)
                                      tttactct  CT-rich tract
                             attacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaatggacatgattattagcctttgggcattttagcatgaacaagatactctgttttccaagttttggattacattgtttactctaatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT