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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAACAAGTCAGAAGGAAGGAGCTATTACTGGTGGTCCTGCTTTTATTGAAGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttctattactctagtttagtatatatatagtgtacttttggaattttgatgcatcatctagtgcccaagacaaaaacaaaactagaggtttggt...

Basic information

species Arabidopsis thaliana
transcript AT1G54780.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G37520.1 (Glycine max), 5'ss of exon 2
ATAACAAGTCAGAAGGAAGGAGCTATTACTGGTGGTCCTGCTTTTATTGAAGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttctattactctagtttagtatatatatagtgtacttttggaattttgatgcatcatctagtgcccaagacaaaaacaaaactagaggtttggt------
 | || |||||||| ||||||||  | |||||||| || |||||| |||||||||| || ||||| || ||||||||||||||||| || || ||||| ||||     ||   |   | || |  | || | | ||| || || |   | |   | |  |  | || |   | | |  |  |  || |||    |||         
GTCACGAGTCAGAAAGAAGGAGCAGTCACTGGTGGCCCGGCTTTTGTTGAAGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTTCCTGgta-----cttgcaagtttgtattatttaca-agagtttaattgtcatagtacaaagatttctataatatactataggattaggaatctacgacttttaaagtaat

upper sequence: AT1G54780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G29810.1 (Glycine max), 5'ss of exon 2
ATAACAAGTCAGAAGGAAGGAGCTATTACTGGTGGTCCTGCTTTTATTGAAGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttctattactctagtttagtatatatatagtgtacttttggaattttgatgcatcatctagtgcccaagacaaaaacaaaactagaggtttggt--
 | || |||||||| ||||||||  | |||||||| || |||||| | |||||||| || ||||| || ||||||||||||||||| || || || || ||||        ||  | |  |||| ||    | || |   | |    |||    |   ||  | || |   | |    |  | ||| |||    ||      
GTCACGAGTCAGAAAGAAGGAGCAGTCACTGGTGGCCCGGCTTTTGTCGAAGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTCCCAGgtacttgcaagtttgtattattta-taagagtttaattgtcatgcacaataccaaaa-attttataatatactattggattagaaatctatcttttaaagca
















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|124824801|gb|EH909667.1|EH909667
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATA
EST: gi|124820171|gb|EH905037.1|EH905037
EST:     TGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: TGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|124709468|gb|EH800870.1|EH800870
EST:     GCTGTTGGTGAAAACATTCTTGATCGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGA
genomic: GCTGTTGGTGAAAACATTCTTGAT-GCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGA
EST: gi|125185022|gb|EL199976.1|EL199976
EST:     AGCTGTTGGTG-AAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATA
EST: gi|125013991|gb|EL086260.1|EL086260
EST:     TCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: TCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|86081744|gb|DR377503.1|DR377503
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGARAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|125048992|gb|EL121261.1|EL121261
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATA
EST: gi|124971574|gb|EL045327.1|EL045327
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGGAGGCG-TATA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACG-AGGCGGTATA
EST: gi|124801705|gb|EH890940.1|EH890940
EST:     AGCTGTTGGTGAAAACATTCCTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGG
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGG
EST: gi|86025160|gb|DR320913.1|DR320913
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAA-TACAACGAGGCGGTATATAGCAGTG
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTG
EST: gi|124954934|gb|EL029990.1|EL029990
EST:     TTGGTGTAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: TTGGTG-AAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|116431679|gb|EG474271.1|EG474271
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|86074858|gb|DR370615.1|DR370615
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|124733809|gb|EH825211.1|EH825211
EST:     TGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: TGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|124751302|gb|EH841432.1|EH841432
EST:     GTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: GTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|86077813|gb|DR373570.1|DR373570
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACAAGGCGGTATATAGCAGTGCGAAAA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|125044567|gb|EL116836.1|EL116836
EST:     AGCTGTTGGTG-AAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|125010981|gb|EL083250.1|EL083250
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATA
EST: gi|124995047|gb|EL067316.1|EL067316
EST:     CCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAAGCGGTATATAGCAGTGCGAAAA
genomic: CCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|124882513|gb|EH961415.1|EH961415
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAA
EST: gi|124790969|gb|EH880648.1|EH880648
EST:     TTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: TTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|86025168|gb|DR320921.1|DR320921
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCNAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGGAAA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCG-AAA
EST: gi|125195708|gb|EL210662.1|EL210662
EST:     TTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGAACGAAAAATACAACGAGGCGGTATATAGCAGTGCGGAA
genomic: TTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGA-CGAAAAATACAACGAGGCGGTATATAGCAGTGCG-AA
EST: gi|125297924|gb|EL312009.1|EL312009
EST:     ATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: ATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|124771149|gb|EH861279.1|EH861279
EST:     GCTGTTGGTGAAAACATTCTTGATGACTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGAC
genomic: GCTGTTGGTGAAAACATTCTTGATG-CTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGAC
EST: gi|124918257|gb|EH992114.1|EH992114
EST:     CTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: CTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|124964651|gb|EL038898.1|EL038898
EST:     CTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: CTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|124855783|gb|EH940220.1|EH940220
EST:     GATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: GATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|124929801|gb|EL007315.1|EL007315
EST:     GCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: GCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|86025171|gb|DR320924.1|DR320924
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
EST: gi|86025167|gb|DR320920.1|DR320920
EST:     AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCG                         TACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA
genomic: AGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttct ... gatggtgcagTACTAGCAACGGACGAAAAATACAACGAGGCGGTATATAGCAGTGCGAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAACAAGTCAGAAGGAAGGAGCTATTACTGGTGGTCCTGCTTTTATTGAAGCTGTTGGTGAAAACATTCTTGATGCTACCGTCTCCGAAAATCTTCCCGgtatggttctattactctagtttagtatatatatagtgtacttttggaattttgatgcatcatctagtgcccaagacaaaaacaaaactagaggtttggt

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa