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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttccaacacttattgtcccggtcttttgttgttacttggtaatccatatacaaaatgtcattaataatgtctctttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG

Basic information

species Arabidopsis thaliana
transcript AT1G27110.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0026g01400.t01 (Vitis vinifera), 3'ss of exon 5
-----gtgagtttccaacacttattgtcccggtcttttgttgttacttgg-taatccatataca--aaatgtcattaataatgtct---ctttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG
     |   |   |    || |  |  |    || |||||    ||   | | ||    |  |   |  ||    | |||||| |    |||||  |||||| || ||||||||||||  ||| |||||||| |||||||||||| ||||||||||||||  ||||   ||||||  ||  || ||||| || | 
taactggttgcagctggaaccttgttcctttctcatttgtaagaacccagattattttcactccttagttgattcttataatggcaggacttttgtgcagTTGTGCCATGTTCTTCAATATGAGTGTCGTTTCAAAGAAGCAGTAGAGTTCATGGAAGAATGCTCATCCTCATGGAGTTTGTGTTCATCTTTCAT
















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|116378181|gb|EG420773.1|EG420773
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428736|gb|EG471328.1|EG471328
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428741|gb|EG471333.1|EG471333
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428746|gb|EG471338.1|EG471338
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428724|gb|EG471316.1|EG471316
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116378186|gb|EG420778.1|EG420778
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428726|gb|EG471318.1|EG471318
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428743|gb|EG471335.1|EG471335
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428737|gb|EG471329.1|EG471329
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428729|gb|EG471321.1|EG471321
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428721|gb|EG471313.1|EG471313
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428745|gb|EG471337.1|EG471337
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
EST: gi|116428731|gb|EG471323.1|EG471323
EST:     CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCC                         TTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC
genomic: CTAGGAAAGGCTGTGAGATCAACGAAAACGATTCTTGGGCTCATCACGCCgtgagtttcc ... tttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttacttggtaatccatatacaaaatgtcattaataatgtctctttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG
                              cattaat  putative branch site (score: 3)
                                       tgtctcttttt  putative PPT
                 atatacaaaatgtcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttccaacacttattgtcccggtcttttgttgttacttggtaatccatatacaaaatgtcattaataatgtctctttttggcagTTATGTCATGTTCTTCAAACTGAATGTCGTTTTAAAGAAGCAGTAAAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC