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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtcatgttggttctaaaccgacccaaaaaaacccgctataccgagaatccaactctttgtgcttagatatctgttaacgttggttgtatgtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCGTATTACAGGAGACTGAAATGGTCAGTACTCAAATCCCGTAAGCTTGTTC

Basic information

species Arabidopsis thaliana
transcript AT5G40810.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 7
cgtcatgttggttctaaaccgacccaaaaaaacccgctataccgagaatccaactctttgtgcttagatatctgttaacgttggttgtatgtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCGTATTACAGGAGACTGAAATGGTCAGTACTCAAATCCCGTAAGCTTGTTC
 ||| ||||  || |    | | |   |     ||  || | ||| ||    || |    |     | | |||    ||  | |||  |||  | |||||||||| || |||||||||||  ||||||| ||||| || ||||| ||||| |||||| |  |  |||  |||||||| || || || || ||||| ||||
-gtc-tgtttcttttgctgctatc---atgtttccaatagatcgataaagacacgc---atatcctgttttctaactacacttgtt--atgcatatgcagATGGGATTTAAATGGATATTTGTACTGTCATTGGCACTACTTCAGGCTGCCTATTACCGCCGCTTGAGGTGGTCAGTTCTAAAGTCTCGCAAGCTGGTTC

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 7
cgtcatgttggttctaaaccgacccaaaaaaacccgctataccgagaatccaactctttgtgcttagatatctgttaacgttggttgtatgtgtg-tgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCGTATTACAGGAGACTGAAATGGTCAGTACTCAAATCCCGTAAGCTTGTTC
 || || | | |||| ||    |          ||  |||   ||| |   || |   | || |||         | || || | | | |      ||||||||||||||||||||||||| ||||| ||  |||| || ||||||||||| |||| |||| || |||  ||||| ||   ||| || ||||||||  || 
-gtaatttggcttctgaattccct-------gtccattatgatgagta--aaatttagtttgttta---------tgactttagatctcttcaaaatgcagATGGGGTTCAAATGGATATTTTTACTTTCACTGGCACTACTTCAAGCTGCTTATTTCAGGCGATTGAGGTGGTCTGTCTACAAGTCTCGTAAGCTGATTG
















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|124706021|gb|EH797423.1|EH797423
EST:     CCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTG                         ATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCT
genomic: CCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTGgtaagtttct ... gtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCT
EST: gi|116466135|gb|EG508727.1|EG508727
EST:     TATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTG                         ATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTTTGCTTCAAGCTGCG
genomic: TATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTGgtaagtttct ... gtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCG
EST: gi|86078839|gb|DR374596.1|DR374596
EST:     TATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTG                         ATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCG
genomic: TATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTGgtaagtttct ... gtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCG
EST: gi|86083864|gb|DR379623.1|DR379623
EST:     TATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTG                         ATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCG
genomic: TATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTGgtaagtttct ... gtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCG
EST: gi|86080213|gb|DR375970.1|DR375970
EST:     TATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTG                         ATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCG
genomic: TATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTGgtaagtttct ... gtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatccaactctttgtgcttagatatctgttaacgttggttgtatgtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCGTATTACAGGAGACTGAAATGGTCAGTACTCAAATCCCGTAAGCTTGTTC
                           tgttaac  putative branch site (score: 2)
                  ttagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtcatgttggttctaaaccgacccaaaaaaacccgctataccgagaatccaactctttgtgcttagatatctgttaacgttggttgtatgtgtgtgcagATGGGGTTCAAATGGATATTCTTACTGTCTTTGGCTCTGCTTCAAGCTGCGTATTACAGGAGACTGAAATGGTCAGTACTCAAATCCCGTAAGCTTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA