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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtggattttgattagatcttgtggtggtaatataaatttggatag

Basic information

species Arabidopsis thaliana
transcript AT2G40590.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G40590.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G39940.1 (Glycine max), 5'ss of exon 2
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtgg-attttgatta--gatcttgtggtg-gtaatataaatttg-gatag
||||||||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||  |||||||||||||||||||||||||||||||||| ||   |||         |||| ||| |  ||  | |    | | |  |||| || | ||  ||||  ||| ||| | |  || | | |||||    | ||
ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgttcttatttcact------ttcttcaacct-tccttttttttttatttttatgcggcaattcaattaaagattttgagatttgtgaaaaaaattaataacag

upper sequence: AT2G40590.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 2
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgt-actctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtggattttgattaga-tcttgtggtggtaatataaatttggatag
|| |||||||| |||||||| ||  | ||||| |||  | | || || |||||    ||| |||||||||||||||||||||||||||| ||||| | | |||   ||  | |||||      |  |||   |   |  |  | | |     |||  ||||   | ||||| | |     | ||   |     
ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAGgttattatctatttcgctttcttccttccaccttcagatttgtgcgaggcatttcaaattttcaattaaccttttgtgctcgccccgtgaaacag-----

upper sequence: AT2G40590.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G14950.1 (Glycine max), 5'ss of exon 2
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt-cctccttctcttctccaatcaa--tcaatctccagtaactcctatgtggattttgattagatcttgtggtggtaatataaatttggatag---
||||| ||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||  ||||||||||||||||||||||||| |||||||| |  ||||   ||  | ||||   |  ||||  |   | | | |   |   |   |  |||||  || |   ||        |||| ||||    |||    
ACTTTTAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGTCCTAAGgttcgttcttatttcactttcttaaacgttcaaatttttttttctgcggcaattcaattaatttttttttgcgatttgtaaaaaaata-aaataataataacag

upper sequence: AT2G40590.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA17G18200.1 (Glycine max), 5'ss of exon 2
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtggattttgattagatcttgtggtggt-aata--taaatttggatag----------------
|| |||||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||| ||||||||||||| |||||||||||||| |||||  | | ||  |  |  | || ||  || | |     | |  |    |   |   |||||     ||   ||    |  | || |  |||  ||   |                  
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAGgt-ttttttttattttattattatc--attatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattttcaacaactaaccttttgtgctcgctctgtgaaacag

upper sequence: AT2G40590.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA14G38950.1 (Glycine max), 5'ss of exon 2
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtgg-attttgattagatcttgtggtggtaatataaatttggatag
|| |||||||| ||||| || ||  | ||||| |||  | | || || |||||    ||| |||||||||||||||| ||||||||||| |||||  | | |       | | ||   |  ||   ||   || | |   |  |  |  | ||||  ||||    |        ||| ||||     |    
ACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGAAAATGCTGCCCCAAGgttgtttttattattatttatttcactttcttccaccttcaaattttttgtgcgaagcatttcaattaa--ttgaaaaaaataaaataataacag----

upper sequence: AT2G40590.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 5'ss of exon 2
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtggattttgattagatcttgtggt----ggtaatataaatttggatag-----
|| |||||||||||||| |||||  | |||||||||  | | || ||||||||    ||  | ||||||||||| ||||||||||||||||||||||| | |     ||| |  |  ||  |||||    ||  | |  ||    | |||     ||  |       |       || || | || |||| ||       
ACGTTCAAGCGAAGGAATGGTGGTCGCAACAAGCACGGCCGCGGCCACGTCAAGTTCATTCGCTGCTCCAACTGTGGCAAATGCTGCCCTAAGgtacttttt-----cttttgcttgcc--tcaattttcctttattttctttcgtttggtggccgagaaatatccataaccataggaaagaaaactttgaatctttttt

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|86018764|gb|DR314510.1|DR314510
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018765|gb|DR314511.1|DR314511
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018763|gb|DR314509.1|DR314509
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAA-AGGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGC
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGG-TTCATTGTGAGGAACATTGTGGAGCAGGCTGC
EST: gi|86018762|gb|DR314508.1|DR314508
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGGAACATTGTGGAGCAGGCTGC
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGG-AACATTGTGGAGCAGGCTGC
EST: gi|86018768|gb|DR314514.1|DR314514
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018759|gb|DR314505.1|DR314505
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|116449486|gb|EG492078.1|EG492078
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGTGGCAAATGTTGCCCCAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018770|gb|DR314516.1|DR314516
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGAAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018767|gb|DR314513.1|DR314513
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018760|gb|DR314506.1|DR314506
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018757|gb|DR314503.1|DR314503
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018758|gb|DR314504.1|DR314504
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018761|gb|DR314507.1|DR314507
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018766|gb|DR314512.1|DR314512
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
EST: gi|86018769|gb|DR314515.1|DR314515
EST:     GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG                         GACAAGGCCATTAASARGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT
genomic: GACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctctt ... atttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAGgtactctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtggattttgattagatcttgtggtggtaatataaatttggatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC