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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaataatcctagtagatatacaagcgttttcaaaagactgaggattaaagtttaataccgttttgtgttatgggttttgtagGAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAG

Basic information

species Arabidopsis thaliana
transcript AT5G18590.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18590.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA17G02680.1 (Glycine max), 3'ss of exon 13
----------gtaaaataatcctagtagatatacaagcgttttcaaaagactgaggattaaagtttaataccgttttgtgttatgggttttgtagGAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAG
           ||    |  |  ||    |  | |   || | ||    |   | | |||   ||||  |  | ||| | |||    | |||||||||||||| ||||||||||||||| |||||||||||||||||||||| |||||  | |||
gtacatgtacatatttgatgcgaagctcctgcatacctgtatacattgtatacatggttat--tttatgattgatttat-ttaaatttgttgtagGAGTTGCACTCAACAAGAGGAGTTATTGCAGGAGAAAGAGCAAGAGCATTCCAACTACAG

upper sequence: AT5G18590.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA07G38020.1 (Glycine max), 3'ss of exon 14
------------------------------------------------------------------------gtaaaataatcctagtagatatacaagcgttttcaaaa--gactgaggattaaagtttaataccgttttgtgtta--tgggttttgta--gGAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAG
                                                                         | | ||  |   |  ||  || ||  |    | || |    |  |   |  |  ||| ||    | |||  |||  |   ||| |||  ||||||||| || |||||||||||| ||||||||||||||||||| || |||||  | |||
gtacatacatattttgttaagatatgatatgatagagatttacgagagatttgataagatatgattttgtttatgatatggtatcaa-agccatgcatcctccatgaagatctgcataatgtgtacattttatgagatattgatttatttaaatttggtaaagGAGTTGCACTCGACAAGAGGAGTTATTGCAGGAGAAAGAGCAAGGGCATTCCAACTTCAG

upper sequence: AT5G18590.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 15
--------------gtaaaataatcctagtagatatacaagcgttttcaaaagactgaggattaaagtttaataccgttttgtgttatgggttttgt---agGAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAG
              | ||  | ||   ||| | |  ||  |   |||  ||   |||  ||   |  ||   ||   || |  |  ||   |||  |   ||||| | |||||||| |||||||| ||||||||||| || |||||||| |||||  |||||
gtttgtagcatcttgcaagttgattgaagttggtg-acttgtaatttataatatctggtgaaccattttatgtaagcttattggaaattcatttcatttcagGAGCTTCATTCAACTAGAGGAGTGCTTGCAGGAGAGAGGGCAAGAGCATTCCAACTGCAG

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|86055075|gb|DR350832.1|DR350832
EST:     TTGAGCATGATGTAGCGTTCCTCAAAGCTGTCCTAGACGATACACAAAAG                         GAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTC
genomic: TTGAGCATGATGTAGCGTTCCTCAAAGCTGTCCTAGACGATACACAAAAGgtaaaataat ... ggttttgtagGAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTC
EST: gi|124707092|gb|EH798494.1|EH798494
EST:     TAGCGTTCCTCAAAGCTGTCCTAGACGATACACAAAAG                         GAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAAGAGCAAGAGCGTT
genomic: TAGCGTTCCTCAAAGCTGTCCTAGACGATACACAAAAGgtaaaataat ... ggttttgtagGAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAA-GAGCAAGAGCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaaaagactgaggattaaagtttaataccgttttgtgttatgggttttgtagGAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAG
                      gtttaat  putative branch site (score: 4)
                attaaagtttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaataatcctagtagatatacaagcgttttcaaaagactgaggattaaagtttaataccgttttgtgttatgggttttgtagGAGTTGCATTCAACAAGAGGAGTTCTTGCAGGAGAAAGAGCAAGAGCGTTCCAGTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA