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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA

Basic information

species Arabidopsis thaliana
transcript AT2G33210.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 3
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
                                                 ||   |     |         | ||| |       | ||      | |||  | |  | |||| |||||    || | |    ||    || ||||||       || || |||| || |||||  | || || || ||||  ||| |||| || || |||||||| ||||||||||||||||||||||||||||||||||||||| | ||||
-------------------------------------------------agcacagtgtttgttgggcctacaactttttatgtttttattt--tgtcag-agtgctgtgttgtgttatttgcagattg---gacttaacgtgtcta-------ttatgcagGGACGCAATGTGGTTATTGAGCAGAGCTATGGTTCACCGAAAGTCACAAAGGACGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAGTCAAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 3
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaaca-atcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
                                                         |  |   | || | |    |       ||| ||    || ||  | ||  |  |  || | |  |  ||| | |      | | ||  |||       | ||| |||| || | |||  | || || |||||||  ||||| || || || ||||||||||| || |||||||||||||||||||| ||||   | ||  ||||||
--------------------------------------------------------gttatgtgagattgcttttttagttttttatggatctttaacagtacattttgggagttatcatgcaaacaatgttgagctcaatataacta-------tgttgcagGGACGCACTGTTGTTATTGAGCAAAGCTTTGGTGCTCCTAAAGTTACAAAGGATGGAGTTACTGTTGCCAAGAGCATTGAATTCAGTAACAGGGTTAAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 2
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaa-gtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
                                               | | ||| || | |      | | |    | ||    |  | | |  ||  |   | | || ||||||||    ||   |||      ||   | || ||         | || |||| || |||||  | || || |||||||  |||||||| || || ||||||||||||||||||||||| ||||||||||| || ||||||||| | ||||
---------------------------------------------actcactgattccaatactgtttggtttgttttactttgttgtaatactgttgccttagttgtttgttttgta---cttgaact------tatcgcctgcct---------tctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
                                                    | |   | | |  |  | ||  | ||| |  || ||     ||   |  | |  |   ||| |||    |   |||      || | | ||          ||| || |||| || |||||  | || || |||||||  |||||||| || || |||||||||||||||||||| || ||||||||||| || ||||||||| | ||||
----------------------------------------------------gcactcactgattataatattgcttgatgtgct-ttactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgc---------tttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgaccta---ttgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaacc---atttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
                                                                      ||  | |   || | |   |||| |  |||||| | | |||  ||   ||    |     |       | |     | | |||      |||||  |||| ||||||||  | || || ||||| |  || ||||| || |||||||| ||||| || || ||||| ||||||||||| |||||||||| | | ||||
--------------------------------------------------------------------gaatgtcttttggatccaggcttgaaacatatcaatagtagtcccttcattttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 3
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
                                                         |  ||     |  ||    |  | |     |    ||  |      |    || | || |    | | |||     |   |  ||           | |||  |||| ||||| ||  |  | || ||||| |  ||||| ||||| |||||||| |||||||| |||||||| || |||||||||||||||||| |||| ||||
--------------------------------------------------------ttgattcttggtgcatcttatttcaattctctattgagggttgg--gttaattgatgtggt----ttatacttaaaaaaggttaatcagcgttttgttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
------------gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaat---agataacgtgacgacctattgaca-agtatcaacaatcgtctgttttgttaccctcacact--ctctgatactac-atgtctaaaaccatttttga-agGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
             |   |  ||   ||||||      ||  |     |   |   ||| |  || | ||||| |  | ||   ||||        ||| ||  | |  ||| | |       |   |    |      |  | |  || | ||      | ||      |  |||   | |||| || | ||| |||||||| |||   |  ||  | || || ||||| ||||||||||| |||||||| || |||||||| |||||||| ||  ||||||
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggt-attctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 1
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgat-actacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
                                                                                              |   | | |||| || |||          |||  ||  |||  ||   | |||    ||   |||| |||| || || ||  | ||||| ||| |||  ||| | || ||||| || ||||||||||||||||||||||||||||| || |||||||| |   | ||||
-------------------------------------------------------------------------------------------gtattctatccatcgcctttttccaatgaacaacaaactaagatcgctctttttctttttcc--ctttgcagGGGCGAAACGTTGTGATCGATCAAGGCTTTGGTTCTCCCAAGGTTACCAAGGATGGTGTGACTGTTGCCAAGAGCATCGACTTCAAGGACAAGCTGAAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 1
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
                                                                                                       |  ||| |    |  || |    |  |     || |  |   |        ||||| |||| || || ||  | ||||| ||| |||  ||| | || ||||| || ||||||||||||||||||||||||||||| || |||||||| |   | ||||
------------------------------------------------------------------------------------------------------gtattctatcc-atcgcctttttccaatgaacaacaaacttcttttttttccttttgtagGGGCGAAACGTTGTGATCGATCAAGGCTTTGGTTCTCCCAAGGTTACCAAGGATGGTGTGACTGTTGCCAAGAGCATCGACTTCAAGGACAAGCTGAAGA

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|116483326|gb|EG525918.1|EG525918
EST:     GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAG                         GGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
genomic: GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAGgtataaactt ... atttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
EST: gi|47829841|gb|CK119525.1|CK119525
EST:     GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAG                         GGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
genomic: GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAGgtataaactt ... atttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
EST: gi|116483327|gb|EG525919.1|EG525919
EST:     GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAG                         GGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG
genomic: GGGGTGTTGAGGATCTTGCTGATGCAGTTAAAGTCACTATGGGACCCAAGgtataaactt ... atttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA
                                   gtctaaa  putative branch site (score: 3)
                                           ccattttt  CT-rich tract
                                             atttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA