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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagtgtgaattttttgagatttgttgcttttgaattaggtgactgaaatgtgaatttgcatatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACAATGGAGGACATACTGACTCAATTGAAGAAGGAGATGGCTGCATCGCATA

Basic information

species Arabidopsis thaliana
transcript AT2G36060.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G36060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G21780.1 (Glycine max), 3'ss of exon 2
------------------------gtaagagt---gtgaattttttgagatttgttgcttttgaattaggtgactgaaat-gtgaatttgcatatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACAATGGAGGACATACTGACTCAATTGAAGAAGGAGATGGCTGCATCGCATA
                        |  | | |   ||  ||||| |  | ||  |  ||  | |  |  |||||   | |  |  | ||| ||  |  ||||| ||  ||||||| |||||  |||||||||| ||||||||| ||||||| ||||||||||||||||| || ||||||||||| ||||| ||  | ||||
gacacttctcatgtttatgattatgagaaaatttagtctattttattggcttaataactaattatctttgtgacaagatttatagacttgaatgaa-atagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA
















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|163979863|gb|ES043410.1|ES043410
EST:     GACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
genomic: GACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
EST: gi|124845906|gb|EH930343.1|EH930343
EST:     GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGACAAACTGGCAAAGACAGTACAC
genomic: GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTG-CAAACTGGCAAAGACAGTACAC
EST: gi|164007349|gb|ES086939.1|ES086939
EST:     GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGC
genomic: GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGC
EST: gi|86078812|gb|DR374569.1|DR374569
EST:     GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
genomic: GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
EST: gi|125214691|gb|EL229011.1|EL229011
EST:     TGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
genomic: TGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
EST: gi|116467250|gb|EG509842.1|EG509842
EST:     GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGCA
genomic: GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCA
EST: gi|125273138|gb|EL287223.1|EL287223
EST:     TGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
genomic: TGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
EST: gi|125073370|gb|EL137728.1|EL137728
EST:     GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTG
genomic: GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTG
EST: gi|125266745|gb|EL280830.1|EL280830
EST:     GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGCTTGGGGTTCTTGCAAACTGGCAAAGACAG
genomic: GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAG
EST: gi|124951717|gb|EL027058.1|EL027058
EST:     TTCCATTCGTTCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGG
genomic: TTCCATTCG--CGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGG
EST: gi|164196005|gb|ES143420.1|ES143420
EST:     GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GGTGGATTCAAAGAAGTTTGGGGTTCTTGC
genomic: GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagG-TGGATTCAAAGAAGTTTGGGGTTCTTGC
EST: gi|124800698|gb|EH890335.1|EH890335
EST:     GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTT
genomic: GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTT
EST: gi|164197157|gb|ES078742.1|ES078742
EST:     GTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
genomic: GTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACA
EST: gi|116466784|gb|EG509376.1|EG509376
EST:     GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTG                         GTGGATTCAAAGAAGTTTGGGGTTCTTGCA
genomic: GGTTCCATTCGCGTATCAACATGACTTGTGTCAACCATGATACCGGCGTGgtaagagtgt ... atatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagatttgttgcttttgaattaggtgactgaaatgtgaatttgcatatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACAATGGAGGACATACTGACTCAATTGAAGAAGGAGATGGCTGCATCGCATA
             ttttgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagtgtgaattttttgagatttgttgcttttgaattaggtgactgaaatgtgaatttgcatatacgtagGTGGATTCAAAGAAGTTTGGGGTTCTTGCAAACTGGCAAAGACAGTACACAATGGAGGACATACTGACTCAATTGAAGAAGGAGATGGCTGCATCGCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG