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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttccactctaaacatctcaaataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag

Basic information

species Arabidopsis thaliana
transcript AT5G03730.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttccactctaaacatctcaaataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag
|||||| || ||||| ||||| ||||| |||||||| || || ||| | ||||||||    |||||||||||||||||| |||  || ||||| ||||||||   ||  |         |     || | |  |||||| |    | || |||       |   ||  |||  | ||  | |||  | |   | | ||                
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgt---ttgtatctcctgttttcttcatcacacggatattttccaac-ttcgga-------cgaactgaattgaacaaagt-ctacctgttcacttgcag---------------

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgt----actttccactctaaacatctcaa-ataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag---------
 ||||| || ||||| ||||| ||||| ||||||||||| || ||||| |||||||||   |||||||| || |||||| |||| |||||||| ||||||||    |  |    || ||  |||| ||  || | | |||  || | | || ||| ||  | || ||      |  || | |  | || | | |  |  || ||||| | || | ||           
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagc-tttagatataccccatggagaaaatccttaagttctctcttttttgtta-aaaaatacgtacaattttacttgcag

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA13G21480.1 (Glycine max), 5'ss of exon 13
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttccactctaaacatctcaaataataatgatattattttgcatttggaagtccc-tcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag
|||||| || ||||| ||||| ||||| |||||||| || || ||||| ||||||||||| ||||||||||| ||||||| ||| |||||||| || |||||   ||  |   ||    |   | || ||| ||   |   |||    ||   ||| |  | | | |   | | || |  || |||   || |  |   |  |            
TGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGCAACAGCCATGGGTTAATTTAAATCCAGCACAGgtttgttgta---tagctgtgatacatgatattgtagtatgtttatgcttaatagttctattattattattattattat-tgttattgttgttgctgttattat-----------

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA03G34890.1 (Glycine max), 5'ss of exon 14
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttccactctaa-acatctcaa-ataataatgatattattttgcatttggaagtccctcactctacatttcat-aacatgctatatatgatcatacaaaaaaatgttccatag
|||||| || ||||| ||||||||||| |||||||| || ||||||||||||||||| || ||||||||||| || ||| |||| || |||||| | |||||   |   ||| | | | || |||   |  | ||| |  |||||| ||||  ||  |   |   |||   ||| || ||  |  ||   |||| ||   |                
TGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCGCCACAGgtttgtataactttgatatatttcagtgtgcttatgcttatattttccattacgac-tatattgttctgatttttatgaaagtcttaggcatgagcaggaa----------------

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA10G07610.1 (Glycine max), 5'ss of exon 15
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttccactctaaacatctcaaataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag
|||||| || ||||| ||||| ||||| |||||||| || || ||||| ||||||||||| ||||||||||| ||||||  ||| |||||||| || |||||   ||  |   ||    |   | || ||| ||   |   |||    ||   |||     | | |   | | || | ||  | |      | ||  |||    ||        
TGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGCAACAGCCATGGATTAATTTAAATCCAGCACAGgtttgttgta---tagctgtgatacatgatattgcagtatgtttatgcttaatagttgt--attattattattattatattttttcagcatttatg-aaacttgtg--------

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA19G37570.2 (Glycine max), 5'ss of exon 14
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttcc---actctaa-acatctcaa-ataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag
 ||||| || ||||| ||||||||||| |||||||| || ||||||||||||||| | || ||||||||||| || ||| |||| || |||||  | |||||   ||     ||| | | | || |||   |  | ||| |   ||||| || |  ||  |   |  || |   ||| || | |   | | || ||||  |                  
CGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgtataactttgatatatttcagtgtgcttatgcttagattttccaatacgat-tatattgctttgatttttatgaaagattctttaagatctga------------------

upper sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 5'ss of exon 13
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttccactctaaacatctcaaataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag
|||| | || ||||||||||||||  | || ||||| ||  | ||||||||||| ||||| |||||||||||||| ||| |||| |||||||| || |||||   ||    ||| ||  | |  |||   | ||| || |||  | |    ||      |   |    |||  |||   | || |  | |   | |  |   |||  |      
TGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAGgt---ttgtcttctgaagttatgtaatgcaagtgaaatcatt--gaaagaagagagagattgttgatgatt--atatttttctttgaaggg--agatgatgcaattctt-----

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|116414933|gb|EG457525.1|EG457525
EST:     GGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAG                         GTTGTAGCTGCGGTTGGTTTCAAGTGTAAACGGCTGGAGATCCCGCGTAAT
genomic: GGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttcca ... tgttccatagGTTGTAGCTGCGGTTGGTTTCAAGTGTAAACGGCTGGAGATCCCGCGTAAT
EST: gi|124983048|gb|EL055806.1|EL055806
EST:     GAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAG                         GTTGTAGCTGCGGTTGGTTTCAAGTGTAAACGGCTGGAGATCCCGCGTAAT
genomic: GAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttcca ... tgttccatagGTTGTAGCTGCGGTTGGTTTCAAGTGTAAACGGCTGGAGATCCCGCGTAAT
EST: gi|116423837|gb|EG466429.1|EG466429
EST:     GGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAG                         GTTGTAGCTGCGGTTGGTTTCAAGTGTAAACGGCTGGAGATCCCGCGTAAT
genomic: GGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttcca ... tgttccatagGTTGTAGCTGCGGTTGGTTTCAAGTGTAAACGGCTGGAGATCCCGCGTAAT
EST: gi|116414934|gb|EG457526.1|EG457526
EST:     GGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAG                         GTTGTAGCTGCGGTTGGTTTCAAGTGTAAACGGCTGGAGATCCCGCGTAAT
genomic: GGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttcca ... tgttccatagGTTGTAGCTGCGGTTGGTTTCAAGTGTAAACGGCTGGAGATCCCGCGTAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgtactttccactctaaacatctcaaataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT