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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatctcttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcatcag

Basic information

species Arabidopsis thaliana
transcript AT4G34050.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os06g06980.3 (Oryza sativa), 5'ss of exon 2
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatctcttcatcctcctctgttttttggtgggttttgtc-gaacttgggaattga--aagtttcatcctttttatcatcag-----
|||  | |||||| |   ||||||||| || ||||||||||| || ||||| |||||||| || ||||||||||| || ||  |||| || |||||||  || |   |  | |     || | ||| ||   | |  | | | |   ||| |    ||| ||   |  | ||||| | |  | |  |      
GCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACGgtcagcaacacgcaaatcccccatctcttccatcgcagatctggcaagaaatccccaatcgattgacgtccatccctctgctaactaatgcag

upper sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G099363_T03 (Zea mays), 5'ss of exon 2
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaat---caatctcttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagt-ttcatcctttttatcatcag------------------------
||| ||||||||| |   ||||||||| || ||||||||||| || ||||| |||||||| || ||||||||||| || || ||||| || |||||||  ||   |   |  |||||   ||   |||| | | ||     | | || |   |      |   |   | || | || | |     ||                          
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccctttctctctttctctctctctctctttcccagatctgccacccacccagaccaaggatctttacccctctctgtctctctctctgttgctcgtccccccgcag

upper sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G127948_T02 (Zea mays), 5'ss of exon 4
-------------------------------------------GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatctcttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcatcag
                                           ||| ||||||||| |   ||||||||| || ||||||||||| || ||||| |||||||| || |||||||| || || || ||||| || |||||||  ||   ||  | |   |  |||  |||    | ||          ||   | ||                                
ACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTActccctcctcgccacggcgctcgccctcccggaggacggcacggtccgtcgttgttccctcccttttctcagatctgccaccccacctc---cctgaaggcga-------------------------

upper sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G127948_T04 (Zea mays), 5'ss of exon 5
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatctcttcatcctcctct---gttttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcatcag--------------------------------------------
||| ||||||||| |   ||||||||| || ||||||||||| || ||||| |||||||| || |||||||| || || || ||||| || |||||||  ||   ||  | |   |  |||  |||    | |           |    |||   |        |    || |||   | || | |                                              
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcag

upper sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G11530.2 (Glycine max), 5'ss of exon 3
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatct---cttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagtttc----atcctttttatcatcag--------
|||  | |||||| | || ||||||||||| ||||| || || || |||||||| || || ||||| ||||||||||| ||||| |||||||| || || |||    || |    |||    | ||       |   |     ||| ||   ||    |||  ||| ||||    | || |||| |   ||         
GCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGATATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtattaaaagcagagcttagcacccccaaagaataaagctttatttttctctctataaaatcaaaattttctgacaaccattttctatgcaattatagtc

upper sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G33780.1 (Glycine max), 5'ss of exon 3
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatctcttcatc--ctcctctgttttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcatcag---------------------------------------------------------------------------------
|||  | |||||| | || ||||||||||| ||||| || || || |||||||| || || ||||| ||||||||||| ||||| |||||||| || || |||    || ||  |  |   |    |  ||| ||  ||   ||   |  |  |||| ||| |    || ||    |  |   |  |                                                                                 
GCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGGTATTCACTTCTTGCCACCGCTCTCGCTCTTCCTGAAGATGGAAAGgtatgaaaagcttcttcttggcaaaaccatttctttatgcaattatactcaaatgggtatttatttattaattacatccaattttgggaaagagtgtccaattatggcatgatgtgttaaacaacaaaaattgtctgaaatttaagttattgtttgtacctggtgcag

upper sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 5'ss of exon 3
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatc-tcttcatcctcctctgtt----ttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcatcag--
|||| |||||||| | || ||||||||||| |||||||| || || |||||||||||||||||||| ||||| || ||||||||||| || ||||| || ||     |||  || |    |  | | ||     |    |   || |     ||  |      |||||         | || ||  |     
GCTTCTCAAGCTCATCAATGCCAAGAACACCATGGAGATAGGCGTCTACACTGGCTACTCTCTTCTGGCCACAGCCCTTGCTCTCCCCGATGACGGAAAGgtcgggaaatggtcatagatcaacacagtaatcatccaagcacgtataaaaaaatgttatggctgaaaaaaattggttcttgattgttgcag

upper sequence: AT4G34050.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ22516 (Selaginella moellendorffii), 5'ss of exon 3
GCTTA-TCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatctcttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcatcag
 |||  ||||| |  | ||||||||||| ||||||||||| ||||| |||||||| ||||||||||||  ||| ||||| ||||| || ||||| || |  |||||   ||||    |       |      |   || | |    || |                                    
-CTTGCTCAAGATGATGAACGCCAAGAAGACAATGGAGATTGGAGTCTACACTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaa---atcttagaaagtataaccagccatacctgtgctgacgcggatgcacag-----------------------------

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|47829433|gb|CK119117.1|CK119117
EST:     CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
genomic: CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|86020813|gb|DR316559.1|DR316559
EST:     CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
genomic: CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|86020787|gb|DR316533.1|DR316533
EST:     CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
genomic: CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|125325128|gb|EL339208.1|EL339208
EST:     CTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACGGAGAGAATTACGAAATTGGGTTTACCGAT
genomic: CTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAA-TTGGGTTTACCGAT
EST: gi|116475760|gb|EG518352.1|EG518352
EST:     CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
genomic: CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|47832008|gb|CK121692.1|CK121692
EST:     CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
genomic: CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|116475771|gb|EG518363.1|EG518363
EST:     CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
genomic: CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|116446874|gb|EG489466.1|EG489466
EST:     CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
genomic: CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|116377761|gb|EG420353.1|EG420353
EST:     CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
genomic: CTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|125246288|gb|EL260373.1|EL260373
EST:     ACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
genomic: ACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|124914254|gb|EH988128.1|EH988128
EST:     AAGACGGCAAA                         ATTCTGGCTATGGATGTCAACAGAGAGAATTACGGATTGGGTTTACCGATC
genomic: AAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATC
EST: gi|124813597|gb|EH898463.1|EH898463
EST:     CTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAA                         ATTCTGGCTATGGATGTTCAACAGAGAGAATTACGAATTGGGTTTACCGAT
genomic: CTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaat ... ttatcatcagATTCTGGCTATGGATGT-CAACAGAGAGAATTACGAATTGGGTTTACCGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATCAAGCTCGTTAACGCCAAGAACACAATGGAGATCGGAGTTTACACTGGCTACTCTCTTCTCGCCACCGCTCTTGCTCTCCCTGAAGACGGCAAAgtaaatcaatctcttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA