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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaatcagattagatgatgtgtgtgttatcaaaagcctaaatttaagttcattgttcgttcttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G06430.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os06g45820.4 (Oryza sativa), 5'ss of exon 3
----CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaatc---agattagatga-------tgtgtgtgtta-tcaaaagcctaaatttaagttcattgttcgttcttgcag---------------
    ||||||||||||| || ||||| ||||||||||| || |||||||||||||||||||||||  | |||||||||||||||||||| ||||| || ||||||||||  | ||||   | ||| | | |       | ||| | ||| |   |   | |||||       | | ||| |   || |                
GATTCAATTGACAGAATAGTGGCTGGTATGGAAGGAACTGTGATGACAGATGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaactattcatatctggaaatgtattctttgtag

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 3
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaatcag---attagatga-------tgtgtgtgtta-tcaaaagcctaaatttaagttcattgttcgttcttgcag---------------
||||||||||||| || ||||| ||||||||||| || |||||||||||||||||||||||  | |||||||||||||||||||| ||||| || ||||||||||  | |||| |   ||| | | |       | ||| | ||| |   |   | |||||       | | ||| |   || |                
CAATTGACAGAATAGTGGCTGGTATGGAAGGAACTGTGATGACAGATGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGTGGgtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaactattcatatctggaaatgtattctttgtag

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os06g45820.3 (Oryza sativa), 5'ss of exon 3
----------------------------------------CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaatc---agattagatga-------tgtgtgtgtta-tcaaaagcctaaatttaagttcattgttcgttcttgcag-------------------------------------------------
                                        ||||||||||||| || ||||| ||||||||||| || |||||||||||||||||||||||  | |||||||||||||||||||| ||||| || ||||||||||  | ||||   | ||| | | |       | ||| | ||| |   |   | |||||       | | ||| |   || |                                                  
CGTGGTCGGACAGCAATTTCCTCAAAGGAGATTGATGATTCAATTGACAGAATAGTGGCTGGTATGGAAGGAACTGTGATGACAGATGGGAAGAGCAAAAgtcttgttgcttaccatgaagttgggcatgcaatttgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaactattcatatctggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaag

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G087598_T02 (Zea mays), 5'ss of exon 2
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtca-gaatcagattagatgatgtgtgtgttatcaaaagcctaaatttaagttcattgttcgttcttgcag-------------------------
| |||||||||||||||||||| |||||||| || || |||||||| ||||||||||||||  | |||||||||||||||||||| ||||| || || |||||||  | | |||    |   ||  | |  | ||        | |||  ||    |     |  |||  |  ||                         
CTATTGACAGAATTGTAGCTGGTATGGAAGGGACCGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatggatcttcctctttgcagagcttctttcttttgtcttaacattggaatgtgattgggttaatttaggttttgattggtttctcagatattc

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 3
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaa-------tcagattagatgatgtgtgtgttatc--aaaagcctaaatttaa---gttcattgttcgttcttgcag--------------
| |||||||||||||| ||||| |||||||| || || |||||||| ||||||||||||||  | ||||||||||||||||| || ||||| || || |||||||  |  |       ||  |  ||||  | | |   ||  |   ||      ||| | |   ||| | | || |||      |              
CTATTGACAGAATTGTGGCTGGTATGGAAGGGACTGTGATGACAGACGGGAAGAGCAAAAGTCTTGTTGCTTACCATGAAGTCGGGCATGCAATTTGCGGgtaagagatgaatcttcctcttaacagatcttttctcctttgccttgaacattagaatgtgattggtttaattttggtttcgattggtttctcagatatc

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA05G26230.1 (Glycine max), 5'ss of exon 3
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaatcagattagatgatgtgtgtgttatcaaaagcct--aaatttaagtt----cattgt---tcgttcttgcag--------------------
| ||||| || ||||| ||||| |||||||||||||| |||||||||||||||||||||||||| || || || ||||||||||| ||||| || ||||||||||    |||  |  |      | ||||| | |  ||| |  |  | |||  | |     || |||   | ||  ||   |                    
CTATTGATAGGATTGTGGCTGGAATGGAAGGAACAGTTATGACAGATGGGAAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaag---aaatttggctgttgtttttgtgtttaagtaaatgtttcaagattgcaatggaagcaatgtgttttgtctttatggctaattatgtaacacttaat

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G09160.1 (Glycine max), 5'ss of exon 3
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaatcagattagatgatgtgtgtgt-----tatcaaaagcctaaatttaagttcattgttcgttcttgcag-----------------------
| ||||| || ||||| ||||| |||||||||||||| ||||||||||||||||||||||| || || || || ||||||||||| ||||| || ||||||||||  | | |  | | || | |||| | |       | |   |||  |  ||  |||     ||||    ||                            
CTATTGATAGGATTGTGGCTGGAATGGAAGGAACAGTGATGACAGATGGGAAGAGCAAAAGTTTAGTGGCATATCATGAAGTTGGTCATGCTATTTGTGGgtaag--aaatttggctcagtttatgtctttaagtaaatgttttaaggttgcatggaagcaaggtgttttgcctaattaggtaaatcatgtaacacttaata

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G05820.1 (Glycine max), 5'ss of exon 3
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaa-tcagattaga----tgatgtgtgtgtta---tcaaaagcctaaatttaagttcattgttcgttcttgcag------------------
| ||||| || ||||| ||||| ||||||||||| || ||||||||||| |||||||||||||| || || || ||||||||||| ||||| || |||||||||| || || ||||  |  |    ||   |  | ||||   |  |       |||  |||     ||||  | | |  |                   
CTATTGATAGGATTGTGGCTGGAATGGAAGGAACTGTGATGACAGATGGAAAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGTGGgtaagccaaaaatcagggtgtagttttgtctttcgagttaatgtttatgattgcaatggaagcaaggtgttattgcctatataaattcacgttacacttg

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G17070.1 (Glycine max), 5'ss of exon 3
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaa-tcag---------attagatgatgtgtgtgttatcaaaagcctaa-----atttaagttcattgttcgttcttgcag-------------------------------------------------------------------------------------------------
| ||||| || ||||| ||||| ||||||||||| || ||||||||||| |||||||||||||| || || || ||||||||||| ||||| || || ||||||| || || ||||         |  | ||||||    ||  | |||     ||      || ||| |||||  | |  |  |  |                                                                                                  
CCATTGATAGGATTGTGGCTGGAATGGAAGGAACCGTAATGACAGATGGAAAGAGCAAAAGCTTAGTGGCATATCATGAAGTTGGGCATGCTATTTGCGGgtaagccaaaaatcagtaaatgtgtacgatatgatggcaatggaagcaaggtgttattgcctatataaattcatgttacacttgtatataaaagtaatccagaaaaaaacaatggttctcattcagaagctgttttttgtaaacaattccaaaaagttgttcttaaatacctatctgtacttgcag

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 5'ss of exon 3
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaatcagattagatgatgtgtgtgttatcaaaagcctaaatttaagttcat--tgttcgttcttgcag------------------------
||||||| || ||||| ||||| |||||||||||||| ||||||||||| |||||||| ||  |||| ||||||||||||||||| |||||||||||||||||||| | |||    |   ||| |   | |  |    |    | |  || |  | | |  || |    |  ||||                        
CAATTGATAGGATTGTGGCTGGAATGGAAGGAACAGTTATGACAGATGGAAAGAGCAAGAGTCTGGTGGCTTACCATGAAGTTGGTCATGCCATATGTGGgtaagtgaaaatatcctgccatgtttcttattctggacattcgccatgttgatatccttcttgataaggccagcagttttacttcaaaactaatttttca

upper sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S118_166V6.1 (Physcomitrella patens), 5'ss of exon 2
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtca-------gaatcagattagatgatgtg---tgtgttatcaaaagcctaaatttaagttcattgttcgttcttgcag----------------------------------------------------------------------------------------------------
||||||||||||| || || || |||||||| || |||||||| || || |||||||| ||  | ||||| ||||| ||||| |||||||| || || |||||||  |        | || |  |  |   | ||   | ||||   | | ||     |||   |  | || | | | |||| |                                                                                                    
CAATTGACAGAATCGTTGCCGGGATGGAAGGTACCGTCATGACGGACGGCAAGAGCAAGAGTCTTGTTGCATACCACGAAGTCGGCCATGCTATCTGCGGgtaagaaacttgtacaattcgggatgtaccgtatggtttttgttcatatatgcagttttttctatgtagtggtggcttttgctggttctttgtagttggaataactgtgaagtgatatcttcacttaggtcaaaaccatttgatttctgtttgctgaagtgtatgtactgtgtattctgtgcag

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|124940374|gb|EL016830.1|EL016830
EST:     AAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGG                         AACATTGACTCCAGGGCA
genomic: AAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcaga ... gttcttgcagAACATTGACTCCAGGGCA
EST: gi|124905666|gb|EH979746.1|EH979746
EST:     TGCCATATGCGG                         AACATTGACTCCAGGGCATGATGCTGTTCAAAAGGTCACGTTGATACCACG
genomic: TGCCATATGTGGgtaagtcaga ... gttcttgcagAACATTGACTCCAGGGCATGATGCTGTTCAAAAGGTCACGTTGATACCACG
EST: gi|86070337|gb|DR366094.1|DR366094
EST:     AAGAGCAAAAGCTTGGTTGCTTACCATGAA-TTG-CCATGCCATATGTGG                         A-CATTGACTCCAGG
genomic: AAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcaga ... gttcttgcagAACATTGACTCCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATTGACAGAATTGTAGCTGGCATGGAAGGAACAGTCATGACAGATGGGAAGAGCAAAAGCTTGGTTGCTTACCATGAAGTTGGCCATGCCATATGTGGgtaagtcagaatcagattagatgatgtgtgtgttatcaaaagcctaaatttaagttcattgttcgttcttgcag

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