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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcatagcttatccgaactaaactccatgtcttttagttgtagctgaaatttccgtctctgacttatctctttttcttttag

Basic information

species Arabidopsis thaliana
transcript AT2G27600.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 3
TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcat---agcttatccgaactaaactccatg-tcttttagttg-tagctgaaatttccgtctctg-acttatctctttttcttttag-----------
 ||  ||||||| || ||||| |||||||||  ||| ||||||||||| |||||||||||||| ||  | |||||||| || ||||| ||||| ||||||||| ||   |||||||   |   |   | | |  ||   |   || || |||||   |     | || ||||     | ||  | ||||           
CTTCATTGATGAAATTGATTCATTGTGTGGTCAACGAGGAGAAGGAAATGAGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaattttagcttatattattaacttttcttaatcaggtgcctgctacctgaatactttaaatgtgtacttggacgtgttattcttagaatgataatga

upper sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 3
TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcatagcttatccgaactaaactccatgtcttttagttgtagctgaaatttccgtc----tctgacttatctctttttcttttag---------------
 || |||||||| ||||||||| | ||||||  |||||||||||| || ||||||||||||||||| ||||| ||||| |||||||| ||||||||||||||    |  ||||  |  | |   |  |  |    |  ||| |  | | | ||  ||     | ||| ||      |  |     ||               
ATTCGTTGATGAAATAGATTCTCTATGTGGTCAACGTGGAGAAGGGAATGAGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaataaatttatg-gtgccatggtgtagatacgctgattggaa-taatactttagttgacatttgaattgcaatatcctgaacaagtcaagaagcttgagt

upper sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G39410.1 (Glycine max), 5'ss of exon 3
TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgc--------atagcttatccg-----aactaaactcca-tgtcttttagttgtagctgaaatttccgtctctgacttatctctttttcttttag---
 ||| |||| || || |||||  ||||||||   ||||||||||| ||||||||||||||||||||||| || |||||||||||||| ||||||||||||||          |||| || |  |     |  |||| | || | | |   |  ||      ||  |  |   ||  | || | |     | | | |    
ATTTATTGACGAAATTGATTCCCTGTGTGGTCAGCGTGGAGAAGGCAACGAGAGTGAAGCTTCAAGACGGATTAAAACAGAGCTTCTGGTGCAGATGCAGgtaatagttttaatagtttgttggtttacatttaaattgcaatatatagcatatgcgcggcaagctgtcaaatcccagttgtatggccatatatgaatgt

upper sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G30910.1 (Glycine max), 5'ss of exon 3
TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcatagcttatccgaactaaactccatgtcttttagttgtagc-tgaaatttccgt-ctctgacttatc----tctttttcttttag-------------
 ||| |||| || || |||||  ||||||||   ||||||||||| || |||||||||||||||||||| || |||||||||||||| ||||||||||||||  |||| || |   |  |        |   ||| | ||| |   |  |   |  |  |    | || ||        ||  |   ||             
ATTTATTGACGAAATTGATTCCCTGTGTGGTCAGCGTGGAGAAGGCAATGAGAGTGAAGCTTCAAGACGGATTAAAACAGAGCTTCTGGTGCAGATGCAGgta-atagttt-taatagtttgttagtttacatttgaattgcaatatatagcatatgcacatcaagttgtcaagacgccttagtcccagttgtatagcccta

upper sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G09300.1 (Glycine max), 5'ss of exon 3
TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcatagcttatccgaactaaactccatgtcttttagttgtagctgaaatttccgtc----tctgacttatctctttttcttttag---------------
 || |||||||| ||||| ||| | ||||||   ||||||||||| || ||||||||||||||||| ||||| ||||| |||||||| ||||||||||||||    |  ||||  |    |   |  |  |   ||| ||| || ||| ||||  ||     | ||| ||   |  |  |     ||               
ATTCGTTGATGAAATAGACTCTCTATGTGGTCAGCGTGGAGAAGGGAATGAGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatttatg-gtgtcatggtgtagttacgttaattggag-tgatattttagttgacatttgaattgcgttatcctgaacaagtcaagaagcttgagt

upper sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 5'ss of exon 3
TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgt-------gcatagcttatccgaactaaactccatgtcttttagttgtagctgaaatttccgtctctgacttatctctttttcttttag------------
 ||  ||||||| ||||| || || |||||    || |||||   ||| ||||||||||||||  |||||||||||||||| || || ||||||||||||||       |  | |  |   |      |     |    ||||  || ||  |   ||||     | |     || | ||||   ||||             
CTTCATTGATGAAATAGACTCCTTATGTGGCCAGCGAGGAGAGTCAAATGAGAGTGAAGCTTCTCGACGTATCAAAACAGAACTACTTGTGCAGATGCAGgtatttgttgtgtggtgtggactggtggagtcttaaacttttttattata--tattatttattattttattacatttattttatctttattttttgcctgca

upper sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ10867 (Selaginella moellendorffii), 5'ss of exon 3
TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcatagcttatccgaactaaactccatgtcttttagttgtagctgaaatttccgtctctgacttatctctttttcttttag
 ||| | || ||||| |||||  |||||||   ||| || ||||| |||||||| || || || ||||| |||||||| |||||||| || |||||||||||    |||       ||   | || | | |||||   ||  ||||           |||  |                    
CTTTATCGACGAGATTGATTCGCTGTGTGGACAACGCGGTGAAGGCAACGAGAGCGAGGCGTCGAGACGAATCAAAACGGAGCTTCTCGTCCAGATGCAGgt----agc-------aaaagagcttcttttctttggtttacagcttgctgagaaaactcacag-------------------

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|124820944|gb|EH905810.1|EH905810
EST:     CAAAACAGAGCTTCTAGTGCAGATGCAG                         GGTGTTGGACACAATGATGAGAAAGTACTTGTACTTGCAGCAACCAATACA
genomic: CAAAACAGAGCTTCTAGTGCAGATGCAGgtgcatagct ... tttcttttagGGTGTTGGACACAATGATGAGAAAGTACTTGTACTTGCAGCAACCAATACA
EST: gi|125282143|gb|EL296228.1|EL296228
EST:     AGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAG                         GGTGTTGGACACAA
genomic: AGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcatagct ... tttcttttagGGTGTTGGACACAA
EST: gi|164113955|gb|ES101349.1|ES101349
EST:     AGAGCTTCTAGTGCAGATGCAG                         GGTGTTGGACACAATGATGAGAAAGTACTTGTACTTGCAGCAACCAATACA
genomic: AGAGCTTCTAGTGCAGATGCAGgtgcatagct ... tttcttttagGGTGTTGGACACAATGATGAGAAAGTACTTGTACTTGCAGCAACCAATACA
EST: gi|47828551|gb|CK118235.1|CK118235
EST:     AGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAG                         GGTGTTGGACACAATGATGAGAAAGTACTTGTACTTGCAGCAACCAATACA
genomic: AGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcatagct ... tttcttttagGGTGTTGGACACAATGATGAGAAAGTACTTGTACTTGCAGCAACCAATACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGTTGATGAGATAGATTCTTTGTGTGGTACACGTGGAGAAGGAAACGAGAGTGAAGCTTCAAGACGTATCAAAACAGAGCTTCTAGTGCAGATGCAGgtgcatagcttatccgaactaaactccatgtcttttagttgtagctgaaatttccgtctctgacttatctctttttcttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG