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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT

Basic information

species Arabidopsis thaliana
transcript AT3G02830.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 3
gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
               |  |  || ||   |  | |  | | | |   | |  ||  |  | |  |||   |       |  ||  |   ||| | ||| |  |  ||||  ||   ||||| ||||||||||| ||||| ||||| ||||||| |||||| |||||||| || ||  |  | |||||||  |||||     ||||    || |||   |
---------------taatgtagctgctta-aagctgtctattagtatatcttatctttgacgacttagcagcattgttttctgtattatttattgtgcttcacctttttttt---cagTATTATTTGAAGACTGGAACATGCAAATTTGGAGCAACATGCAAGTTTCACCACCCCCGAGAAAAAGCTGCAATTGCAACCCGAGTACAGCTGAATGCTT

upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g21700.1 (Oryza sativa), 3'ss of exon 3
gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaa-actaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
               || | |  |  |   |  | ||| |   |   ||| ||| |  |     ||| |||||    |  ||| | |   || | | | |  ||| || || |    |||||||| ||||| || ||||| ||||||||||| | |||||| ||||||||||| || ||| | || ||||   ||||     | ||     | ||| |  
---------------ttatgcc-tcatcttttgatattctacta---ttttgtactgaaactggctt-ttacatgtcatgaacgttatgcttagagttctcatattttctgctctttcagTACTACTTGAAAACTGGAACGTGCAAGTTTGGTGCAACATGCAAGTTTCATCACCCCAGGGAGAAGGCTGCACTTGCAAACCGTGTACAGTTAAATGTTC

upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G146514_T02 (Zea mays), 3'ss of exon 3
gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
              |||||||  || ||  ||| ||| |  |     ||||| || ||  |  |    |||        || ||    |||| | || ||  ||       ||    |||||||| ||||||| || || ||||||||||||| ||| || ||||||||||||||  |  | || ||||  || ||     ||||     | |||    
------------attttgtccttttctatgtgagcatataatttct-tttggaaagtgtttggttacattatt--ggtgaatttgcatttttattgtttt-catacccccttt---tagTACTATCTGAAGACTGGCACGTGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGTTGAATGAAC

upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G100794_T01 (Zea mays), 3'ss of exon 3
gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaacttaacattttgtggtgttgt-atgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
                       ||| | ||   |   || ||     |  || |||   || | || ||  | |   ||   | ||||| | |  |||| | |  |      |    |||||||| ||||||| || || ||||||||||||| ||| || ||||||||||||||  |  | || ||||  || ||     ||||    || |||    
-------------------ttgcttgcacattttctgcttttcttttctgtgttattatatcgtttt-ttggaaagtgtatggtcacattatttattgttttcacatccctcctttttagTACTATCTGAAGACTGGCACATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAAC

upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 3
gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT-
     ||| || |  |||      | || ||      | |||    ||    | |   | ||| | | ||||| | ||| | |     ||||||| | |                 ||||||||||||||||||||||| ||||| |||||||  ||||| | |||||||||||| ||  |||| ||||||||||||||||||||  |  | ||||| | 
----taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaaacattcaccatattacaaatactgattcccttttttgtgctttc----------------cagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT

upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 3
gtaagaatctttggtttgtccagttgtag-atgaacattttgtcaaggtttg-gtaattgag---tcatcttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
        ||    || |||  | | ||| ||  | ||  | |     |||| | | || |    ||| | | ||||| | ||| | |     ||||||| | |                 ||||||||||||||||||||||| ||||| |||||||  ||||| | |||||||||||| ||  |||| ||||||||||||||||||||  |  | ||||| |
--------ctaattttggtcttgatatagtatatatatcatatatgtatttgtgcatttaaacattcaccatattacaaatactgattcccttttttgtgctttc----------------cagTACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCATGAATATTT

upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
------gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
         ||  |||     |||| | |  ||  | || ||||   |      |||| |         | ||   |||   || || | | |||      || || |      || ||    |||||||| ||||||||||||| ||||| |||||||  ||||| || ||||||||||| |   |  | ||||||||||||||||||||  |  | ||||| |
gcacgtactagtttctcaaccttgtactgcagtgca-gagcattaatttgtatcttggcatgcattctttatttaaacattcaccaa-tcatcataacagagttttttcc-ccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT

upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
------gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagt---catcttcttacacaaactaacttaacattttgtggtgttgtatgtttt-----ggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
         ||  |||     || | | |  ||  | || || |   |     ||| |||  |  |    ||||||  |  | | | | ||  | | |  |       ||| | ||||     |  |   ||||||||| ||||||||||||| ||||| |||||||  ||||| || ||||||||||| |   |  | ||||| ||||||||||||||  |  | ||||| |
gcatgtactagtttctcaaccttttactgcagtgca-gagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT

upper sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 3
gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaactt--aacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
                       |  |      | ||  |||  | | |   || ||      | || | | |    || | ||  || | ||       |||  |    |||||   |||||||| |||||||||||||| |||||||||||||  ||||| |||||||||||||| ||  |||| ||||| |||||||||||||| ||| | ||||| |
---------------------tttaatgtcctcatatcatgtgtaagatctctattttctcatttttttaatatgttctgagttggaagagttgacaaatttgctttgaatggttctccagTACTACTTGAAGACAGGAACTTGCAAGTTTGGAGCCACATGCAAGTTTCATCATCCTAGAGACAAGGCTGGAATTGCTGGAAGAGTTTCTTTAAATATTT

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|164227901|gb|ES023012.1|ES023012
EST:     CAAGGATGAGAGGAGAATACCCTGAAAGGATTGGTCAGCCTGAATGCGAG                         TACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAA
genomic: CAAGGATGAGAGGAGAATACCCTGAAAGGATTGGTCAGCCTGAATGCGAGgtaagaatct ... ggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAA
EST: gi|86037524|gb|DR333279.1|DR333279
EST:     CAAGGATGAGAGGAGAATACCCTGAAA-GATTGGTCAGCCTGAATGCGAG                         TACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCAT
genomic: CAAGGATGAGAGGAGAATACCCTGAAAGGATTGGTCAGCCTGAATGCGAGgtaagaatct ... ggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT
              taacttaacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA