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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtatggaattattacccctctgataatgatttttgttctcattcaactgagtcttagagtttcaaactttctcctgtag

Basic information

species Arabidopsis thaliana
transcript AT1G55490.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 3
TGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtatggaattattacccctctgataatgatttt-tgttctcattcaactgagtcttagagtttcaaactttctcctgtag---------------------------------------------------------------------------------------------------------
 ||||| || || ||||| || |||||||| |||||||| |||||||||||||||||||||||   |||||| ||||||||||| || |||||||  ||||||||  |    ||     ||| |  || | || || |   || | |      |||| |  |||| | |||       |                                                                                                          
CGTTGGAGTCACCCTTGGTCCAAAAGGACGGAATGTTGTCCTTGAGAGCAAGTATGGATCACCTAAAATTGTCAATGATGGTGTTACCGTTGCAAAGGAGgtatgccacgtatagtaaactgttcgtgttcttatgatgcaatcctatcattgcttaaa--ttcagagttttctgaaaaatgactgaacatttggcataaactgtttgttttcttatgatgcaatcctatcatagcttaaattcagagttttctgaaaaatgagtgaacatttggcatgcaccag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 3
TGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtat------ggaattattacccctc-tgataatgatttttgttctcattcaactgagtcttagagtttcaaactttctcctgtag---------------
|||||| |||||||| ||||| || ||| | ||||||||| | |||||||||||||| || ||  | ||||| ||||||||||| || ||||||||||||||||      |   ||||| |  |   |   | ||| |||  ||   |||    ||  |  |  | |   | |||| | |    |                
TGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCAATGATGGTGTTACAGTTGCAAGAGAGgtatattacagtgtttattgcgtcaaatagcattgaatttccttacaatttgcttgtttgctgta-tgctatacttccacagaaaaaaaatgtttgttttg

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 3
TGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgt----atggaattattacccctctgataatgatttttgttctcatt-caactgagtcttagagtttcaaactttctcctgtag-----------------------------------------
 || || ||||| |||||||| || || |||||||| || || || ||||||||||| |||||   |||||| ||||||||||| ||||| ||||  |||||    ||   | ||  | |   |      |  || ||| ||  | | ||||     | |      || |||||  |   |  |                                         
CGTCGGGGTTACTCTTGGACCAAAGGGGCGAAATGTAGTCCTCGAAAGCAAGTATGGCTCACCTAAAATTGTCAATGATGGTGTCACTGTGGCAAAGGAGgtgcacatctgactacaaacttaccatcgtttgttcttgctcgtactgcaaccataccctg----ctctaacttcttgtggctgccgagtttcctcatatgttctgggctgtggccatgcaccag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G133698_T03 (Zea mays), 5'ss of exon 3
TGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtatgga--attattacccctctgataat--gatttttgttctcattcaactgagt-cttagagtttcaaa--ctttctcctgtag-------------------------------------------------------------
                         ||| | ||||||||| | |||||||||||||| || ||   ||||||||| |||||||| || ||||| |||||||||  |   | | |||||    |  || |  || |||  ||   |        | | | ||  |||  | |   ||| | ||  |                                                              
------------------------GGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTAACGATGGTGTTACAGTTGCCAGAGAGGTACAGTGCAATGTTACCATGGTTgtacttagaatttgattgctagctcgtaaattacataacgttgtatatatttttttctccaattcttgtcatacatgttttacaggtcatattcttataacccatgtaatgcatatactttag

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 2
TGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgt-atggaattattacccctctgataatgatttttgttctcattcaactgagtcttagagtttcaaac---tttctcctgtag-------------------
 ||||| || || ||||| ||||| ||| ||||||||||||| |||||||||||||| || ||   ||| ||||| || ||||| ||||| || | |||||| |     || ||     | |  |  | | | ||||| |  ||    |   | || || ||| || |   |   |  ||||                    
GGTTGGGGTCACGCTTGGTCCCAAGGGAAGAAATGTTGTTCTCGAGAGCAAGTATGGCTCGCCGAAAATCGTTAACGACGGTGTCACTGTCGCTAAAGAGgtgactttttttttttgaattttgtcgt-actattgttatggtt-gtttcttttttcgaatttaaagcaggtaattattgtaaaaaccgacaaacttatcat

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 3
TGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtatggaa----ttattacccctctgataatgatttttgttctcattcaa-ctgagtct----tagagttt-caaactttc--tcctgtag---------
 || || ||||| ||||| || |||||  | |||||||| || |||||||||||||| || |||  |||||||||||||||||| ||||| || | |||||||||  |     |||||    | |   | |  |  || | ||  || ||  ||| | |     | ||    ||  || |   |  |||           
AGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTAATGATGGTGTAACTGTGGCCAAAGAGgtatgttaagttctattaattttttttaagttctagttttgcttttttaagttgaatatggaacaaagccagcaggctataagttttgtcaatttctctt

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|47830371|gb|CK120055.1|CK120055
EST:     AGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAG                         GTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAA
genomic: AGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtatggaatt ... tctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAA
EST: gi|164016063|gb|ES176456.1|ES176456
EST:     GATGGTGTGACTGTTGCAAGAGAG                         GTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAA
genomic: GATGGTGTGACTGTTGCAAGAGAGgtatggaatt ... tctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAA
EST: gi|125265165|gb|EL279250.1|EL279250
EST:     TCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAG                         GTTGAGTTGGAAGACCCGGTTGAGAACATT
genomic: TCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtatggaatt ... tctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtatggaattattacccctctgataatgatttttgttctcattcaactgagtcttagagtttcaaactttctcctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA