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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttgctagatcttataacaaaattgggattcattattgtcatgaagaaatgtttattgttgtttttgttgttgtgtaacttagtgttgttatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G48580.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G10750.1 (Glycine max), 3'ss of exon 3
gtaagtttttgctagatcttataacaaaattgggattcattattgtcatgaagaaatgtttattgttgtttttgttgttgtgtaacttagtgttgttatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG
 | |  | |   |  || |  | |    ||  ||| ||||  |  |||   ||   |||| ||  |  | ||   | || | ||  | | |  ||||     |||||| ||||| |||||||||||||| |||||||| || ||||||||   | ||||  |||| ||| |  | || | |||||| || |||||||
ttcaaatctcattttatttgttcatgtgatgaggaatcatc-tactcacttagttttgttgatcatgttcttgcatattatata-ttcactcgtgttt----gcagGGAAAACTCACTGATGGAACTGTTTTCGATTCTAGCTTTGAAAGAAATAATCCAATTGAATTTGAGCTTGGTACTGGTCAAGTGATCAAAG

upper sequence: AT5G48580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G21680.1 (Glycine max), 3'ss of exon 3
gtaagtttttgctagatcttataacaaaattgggattcattattgtcatgaagaaatgtt-tattgttgtttttgttgttgtgtaactta-gtgttgttatgtg-gcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG
         |   | | || || |     ||   ||        |||||| |   |  |  | |||||| |  |||| | |  ||   ||  |    | ||||  |||||| ||||| |||||||||||||| |||||||| || ||||||||   | ||||  |||| ||| |  | || | |||||| || |||||||
---------tttcaaaactcatcattttgttcatatgatgaggggtcatgtattcacttagttttgttgatcatgttctagcatattatatattcactcatgtttgcagGGAAAACTCACTGATGGAACTGTTTTCGATTCTAGCTTTGAAAGAAATAATCCAATTGAATTTGAGCTTGGTACTGGTCAAGTGATCAAAG

upper sequence: AT5G48580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0260g00060.t01 (Vitis vinifera), 3'ss of exon 3
-gtaagtttttgctagatcttataacaaaattgggattcattattgtcatgaagaaatgtttattgttgtttttgttgttgtgtaacttagtgttgttatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG
 ||    ||| ||   |  |  |||   | ||  |    | |  |  |||   |   | |    | ||   ||   || |||| |  ||    || |  |  ||||||||||||| || ||||||||||| || ||||| ||||||||||||||||| ||  |||||||| || | || ||||| || || || ||||
tgtgtactttagc---agttcgtaattgatttttg-ccaaatgctcccattttggtttttcctatatttccttaactgatgtg-agtttttgattatctt--ggcagGGGAAACTCACAGATGGAACTGTTTTTGATTCCAGTTTTGAAAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG

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|116482915|gb|EG525507.1|EG525507
EST:     CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGG                         GGGAA-CTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
genomic: CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
EST: gi|86081492|gb|DR377249.1|DR377249
EST:     CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGG                         GGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
genomic: CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
EST: gi|124722350|gb|EH813752.1|EH813752
EST:     TGCACTATAGG                         GGGAAACTTACTGATGGAACTTGTATTCGATTCGAGTTTTGAAAGGGGTGA
genomic: TGCACTATAGGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAAC-TGTATTCGATTCGAGTTTTGAAAGGGGTGA
EST: gi|164128008|gb|ES072960.1|ES072960
EST:     TACGATCAAGGTGCACTATAGGG                         GGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGA
genomic: TACGATCAAGGTGCACTATA-GGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGA
EST: gi|164053533|gb|ES115447.1|ES115447
EST:     GGTGCACTATAGG                         GGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTTGA
genomic: GGTGCACTATAGGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGT-GA
EST: gi|164067796|gb|ES216355.1|ES216355
EST:     CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGG                         GGGAAACGTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGG
genomic: CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGGgtaagttttt ... tatgtggcagGGGAAAC-TTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGG
EST: gi|164182996|gb|EL988568.1|EL988568
EST:     GGTGCACTATAGG                         GGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
genomic: GGTGCACTATAGGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
EST: gi|116469680|gb|EG512272.1|EG512272
EST:     CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGG                         GGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
genomic: CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
EST: gi|125103707|gb|EL158014.1|EL158014
EST:     TGCACTATAGG                         GGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
genomic: TGCACTATAGGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
EST: gi|86084981|gb|DR380740.1|DR380740
EST:     CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGG                         GGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
genomic: CATGTGAAGTTCAGGCTCACAAAGGTGATACGATCAAGGTGCACTATAGGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
EST: gi|124746138|gb|EH836638.1|EH836638
EST:     AAGTTCAGGCTCACAAAGGTGATACGATTCAAGGTGCACTATAGG                         GGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT
genomic: AAGTTCAGGCTCACAAAGGTGATACGA-TCAAGGTGCACTATAGGgtaagttttt ... tatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaatgtttattgttgtttttgttgttgtgtaacttagtgttgttatgtggcagGGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAG
                            gtgtaac  putative branch site (score: 3)
       tttattgttgttttt  TA-rich tract