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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaattgacagttgccattattacatctgcaattagaagttgttataaaagcttaatccgaagtttgaacccagctgacctaggttgagtttgtatgtagGTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATTGACAAAAACAAGAACACACCATTGCACTATGCTGCTGGTTATGGAAGGA

Basic information

species Arabidopsis thaliana
transcript AT2G17390.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G800734_T02 (Zea mays), 3'ss of exon 6
gaaattgacagttgccattattacatctgcaattagaagttgttataaaagctta-atccgaagtttgaacccagctgacctaggttgagtt---tgtatgtagGTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATTGACAAAAACAAGAACACACCATTGCACTATGCTGCTGGTTATGGAAGGA
  | | || ||    |  | |      |||  ||    |||  | |  |   ||| ||    |  ||     || || |  |  || | |||   | ||| ||| |||  |||||  |  |||| || || || || ||    |   ||||  | || || ||||||||||| || ||||||||||||||||| |||||  |||
--agtcgagagcatgcggtgtagtga-tgcgtttgtttgtttatttgcatatttagatatctatattagtggcaactaat-tgagtggtgttctgtatatttagTTGAAGTGTGCAGAAATTCTCCTTGAGGCGGGGGCCGCAGTTGATGCCCTAGATAAGAACAAGAACACTCCGTTGCACTATGCTGCTGGGTATGGTCGGA
















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|125246210|gb|EL260295.1|EL260295
EST:     CTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG                         GTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAAT
genomic: CTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAGgtatgtcaac ... ttgtatgtagGTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAAT
EST: gi|86081509|gb|DR377266.1|DR377266
EST:     AAGACTCTGAGGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG                         GTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATT
genomic: AAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAGgtatgtcaac ... ttgtatgtagGTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATT
EST: gi|301502460|gb|HO208000.1|HO208000
EST:     AAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG                         GTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATT
genomic: AAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAGgtatgtcaac ... ttgtatgtagGTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATT
EST: gi|125203249|gb|EL218203.1|EL218203
EST:     AAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG                         GTGAGATGTGCTACAGGTTCTTCTGGATG
genomic: AAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAGgtatgtcaac ... ttgtatgtagGTGAGATGTGCT-CAGGTTCTTCTGGATG
EST: gi|125232435|gb|EL246520.1|EL246520
EST:     GCATTTTGCATGTGGATACGGCGAG                         GTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATT
genomic: GCATTTTGCATGTGGATACGGCGAGgtatgtcaac ... ttgtatgtagGTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATT
EST: gi|125032923|gb|EL105192.1|EL105192
EST:     TTTGCATGTGGGTACGGCGAG                         GTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATT
genomic: TTTGCATGTGGATACGGCGAGgtatgtcaac ... ttgtatgtagGTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagcttaatccgaagtttgaacccagctgacctaggttgagtttgtatgtagGTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATTGACAAAAACAAGAACACACCATTGCACTATGCTGCTGGTTATGGAAGGA
                           agctgac  putative branch site (score: 3)
                                            tttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaattgacagttgccattattacatctgcaattagaagttgttataaaagcttaatccgaagtttgaacccagctgacctaggttgagtttgtatgtagGTGAGATGTGCTCAGGTTCTTCTGGATGCTGGAGCAAATGCAAATGCGATTGACAAAAACAAGAACACACCATTGCACTATGCTGCTGGTTATGGAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - ataaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacccag