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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatttggttgtttttacagttttagtggtgaggacgaagaatagtgtaaaatgtctcttctctgttctaattttctttcatttgttgctcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG

Basic information

species Arabidopsis thaliana
transcript AT5G60540.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G60540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G28830.1 (Glycine max), 3'ss of exon 1
-----tagatttggttgtttttacagttttagtggtgaggacgaagaatagtgtaaaatgtctcttctctgttctaattttctttcatttgttgctcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG
      |  |||     || |||   |  || |  |  |  ||  |||    || |    |   ||   | ||  |  ||| | |    ||||    |||| | |||||| ||| |||| ||||||||  | ||||| || ||||||||||| || || ||||| ||||||||||||||| | | |||  | |
gctttgaactttacacattcttaacataataatcttatgctcgtggaaccaagtga----tgattttggtattggagatttatgttggatgttatgattttca-gTTTCCTGCTTTACGAGAGTTTGTACAAATGGGAAAGCCTGTTTGGGGAACCTGTGCAGGGCTTATATTCTTGGCAAATAAAGCTATGG

upper sequence: AT5G60540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G08260.2 (Glycine max), 3'ss of exon 2
----tagatttggttgtttttacagttttagtggtgaggacgaagaatagtgtaaaatgtctcttctctgttctaattttctttcatttgttgctcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG
     |  |||      | |||  ||| ||    |  |  |   |||    || |    |   ||   ||||     ||| | |    ||||    ||||  ||||||| ||| | || ||||||||  | ||||| || ||||||||||| || || ||||| ||||||||||||||| | | |||  | |
ctttgaactttacacactcttaacgttataactttatgctcatggaaccaagtga----tgattttggtgttggtgatttatgttggatgttatgatttttcagTTTCCTGCTTTGCGAGAGTTTGTACAAATGGGAAAGCCTGTTTGGGGAACCTGTGCAGGGCTTATATTCTTGGCAAATAAAGCTATAG

upper sequence: AT5G60540.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g03000.t01 (Vitis vinifera), 3'ss of exon 2
tagatttggttgtttttacagtttta--gtggtgaggacgaagaatagtgtaaaatgtctcttctctgt--tctaattttctttcatttgttgctcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG
      || || ||| |  | ||  |  |   ||||    |    |  | |    |  |  ||| | |    | ||      || |  | ||  |   ||  ||||||| ||| | || |||||||||||  | ||||| ||||||||||| || || ||||| ||||| ||||||||| | |  || ||||
----gctgattctttctgtaattccaaagcaatgagtcgaatacttttttttttttaacctttcgcagcagccaaacaaaacttaaccttttttttgcttccagTTTCCTGCTTTGCGAGAGTTTGTTAAACTTGGGAAGCCTGTTTGGGGAACCTGTGCAGGACTTATCTTCTTGGCAAATAAGGCTGTTG

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|86052477|gb|DR348234.1|DR348234
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTAC
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTAC
EST: gi|86052475|gb|DR348232.1|DR348232
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
EST: gi|86052476|gb|DR348233.1|DR348233
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
EST: gi|47828146|gb|CK117830.1|CK117830
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
EST: gi|86052480|gb|DR348237.1|DR348237
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
EST: gi|86052481|gb|DR348238.1|DR348238
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         A
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaag-
EST: gi|86052481|gb|DR348238.1|DR348238
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         A
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaag-
EST: gi|86052481|gb|DR348238.1|DR348238
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         A
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaag-
EST: gi|86052481|gb|DR348238.1|DR348238
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         A
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaag-
EST: gi|19877313|gb|AU238144.1|AU238144
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
EST: gi|86052483|gb|DR348240.1|DR348240
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTNGGGGACA
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
EST: gi|86052478|gb|DR348235.1|DR348235
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
EST: gi|86052482|gb|DR348239.1|DR348239
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
EST: gi|86052484|gb|DR348241.1|DR348241
EST:     CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTG                         TTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA
genomic: CTGGCGGCGAGAGCACCACCATGGCCAAACTCGCCGAGTATCATAACTTGgtccgctcct ... tcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtaaaatgtctcttctctgttctaattttctttcatttgttgctcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG
                     ttctaat  putative branch site (score: 2)
                           ttttctttcatttgtt  CT-rich tract
                        taattttctttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatttggttgtttttacagttttagtggtgaggacgaagaatagtgtaaaatgtctcttctctgttctaattttctttcatttgttgctcttttgaagTTTCCGGCTCTACGTGAGTTTGTTAAGATGGGGAAACCTGTTTGGGGGACATGCGCAGGTCTTATATTCTTGGCAGACAGAGCAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- gatttgg
- - - - - - - - - - gttttag
- - - - - - - - - - - - - - - - - - cgaagaa