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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACATCAGCGATTGCAGCTGCCTTTGGAGGAGGCTTGCCTCCGGGTATAACCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaagttggtcatttcccgttttgcttttgataacttagtttttcttacaatattttccaaacttaccagattcatttgtttcag

Basic information

species Arabidopsis thaliana
transcript AT1G43190.3
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G43190.3 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA02G08870.2 (Glycine max), 5'ss of exon 7
CACATCAGCGATTGCAGCTGCCTTTGGAGGAGGCTTGCCTCCGGGTATAACCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaagttggtcatttcccgttttgcttttgataacttagtttttcttacaatattttccaaacttaccagattca---tttgtttcag
  |  |||| ||||||||||||||||| ||||| |||||||| || ||||| || |||||||| ||||||||||| |||||| | || || ||| | ||||| |||  |     |     |||     |  |  ||      ||||  | || |||   |||  ||   |  |     ||| || |||
TGCTGCAGCAATTGCAGCTGCCTTTGGGGGAGGTTTGCCTCCTGGCATAACTGGAACAAATGAAAGGTGTACAGTTCTTGTCGCAAATCTCAATCCCGATgtgagtatgctgccttgatatttctgccttttttctagaaagttctctccatttttattaaatatatttggcttgaatttttttccag

upper sequence: AT1G43190.3 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA16G27970.1 (Glycine max), 5'ss of exon 11
CACATCAGCGATTGCAGCTGCCTTTGGAGGAGGCTTGCCTCCGGGTATAACCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaagt--------tggtcatttcccgttttgcttttgataa----cttagtttttcttacaatatttt-ccaaacttaccagattcatttgtttcag------------
  |  | || ||||||||||||||||| ||||| |||||||| || ||||| || |||||||| ||||||||||| |||||  | || || ||| | |||||||||        |||  |||||  |  ||  || ||| |     ||   ||||| | |  ||||||  |   | ||      ||| ||| | |               
TGCTGCGGCAATTGCAGCTGCCTTTGGGGGAGGTTTGCCTCCTGGCATAACTGGAACAAATGAAAGGTGTACAGTTCTTGTTGCAAATCTCAATCCTGATgtaagtacactgcctggatatttct-gccttttttctgaaagttctctccatttttttaaatatatttggcttgagttttttttttcttttttcttttttctttttccag

upper sequence: AT1G43190.3 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA10G36770.1 (Glycine max), 5'ss of exon 12
CACATCAGCGATTGCAGCTGCCTTTGGAGGAGGCTTGCCTCCGGGTATAACCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaagttggtcatttcccgttttgcttttgataacttagtttttcttacaatattttccaaacttaccagattcatttgtttcag
  |  |||| ||||||||||||||||| |||||  ||||||| || ||||| || |||||||| ||||||||||| ||||| || || || ||| | ||||||||       | ||  ||||   | | || |  |   |   | |  ||   | ||   | |||  || ||   ||| ||||||
TGCTGCAGCCATTGCAGCTGCCTTTGGGGGAGGTCTGCCTCCTGGAATAACTGGGACAAATGACAGGTGTACAGTTCTTGTATCAAATCTTAATCCTGATgtaagc--actgtgtctggtttca-tctagaaagttctctccatttctcagcttattt--agctt--caaatatgtttatttcag

upper sequence: AT1G43190.3 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 13
CACATCAGCGATTGCAGCTGCCTTTGGAGGAGGCTTGCCTCCGGGTATAACCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaagttggtcatttcccgttttgcttttgataacttagtttttcttacaatattttccaaacttaccagattcatttgtttcag
  |  |||| ||||||||||||||||| |||||  | ||||| || ||||| || |||||||| ||||||||||| ||||| || || || ||| | ||||||||       | ||  | |||   ||  | ||| |  |||  ||| |     ||    | |||  || ||   ||| ||||||
TGCTGCAGCCATTGCAGCTGCCTTTGGGGGAGGTCTACCTCCTGGAATAACTGGGACAAATGACAGGTGTACAGTTCTTGTATCAAATCTTAATCCTGATgtaagc--actgtgtctggcttt---ttctagaacattctttccctttctcagcttatttagctt--caaatctgtttatttcag

upper sequence: AT1G43190.3 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 5'ss of exon 12
CACATCAGCGATTGCAGCTGCCTTTGGAGGAGGCTTGCCTCCGGGTATAACCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaag--ttggtcatttcccgttttgcttttgataa--cttagtttttcttacaatattttccaaacttaccagattcatttg---tttcag-----------------------------------------------
  | || || ||||| ||||||||||||||||| ||||| || || || |  || |||||||| |||||||| |||||||||||||| || ||| | || ||| |  ||    | |  || || | ||| |  |    |||  | ||  |||     |||||| |  ||| |   |  |||     |||| |                                               
TGCGTCTGCCATTGCTGCTGCCTTTGGAGGAGGTTTGCCCCCTGGAATTAGTGGGACAAATGACAGGTGTACTGTCCTTGTCTCTAATCTAAATCCTGACgtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcag

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|124933281|gb|EL010451.1|EL010451
EST:     CCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGAT                         AGTATTGATGAAGATAAGCTATTCAATCTATTTTC
genomic: CCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaagttggt ... tttgtttcagAGTATTGATGAAGATAAGCTATTCAATCTATTTTC
EST: gi|124982461|gb|EL055269.1|EL055269
EST:     CCTGAATGCAGAT                         AGTATTGATGAAGATAAGCTATTCAATCTATTTTCTCTTTACGGGAACATT
genomic: CCTGAATGCAGATgtaagttggt ... tttgtttcagAGTATTGATGAAGATAAGCTATTCAATCTATTTTCTCTTTACGGGAACATT
EST: gi|125208893|gb|EL223847.1|EL223847
EST:     CCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGAT                         AGTATTGATGAAGATAAGCTATTCAAT
genomic: CCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaagttggt ... tttgtttcagAGTATTGATGAAGATAAGCTATTCAAT
EST: gi|47829251|gb|CK118935.1|CK118935
EST:     CCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGAT                         AGTATTGATGAAGATAAGCTATTCAATCTATTTTCTCTTTACGGGAACATT
genomic: CCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaagttggt ... tttgtttcagAGTATTGATGAAGATAAGCTATTCAATCTATTTTCTCTTTACGGGAACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACATCAGCGATTGCAGCTGCCTTTGGAGGAGGCTTGCCTCCGGGTATAACCGGCACAAATGATAGGTGTACAGTCCTTGTCTCTAACCTGAATGCAGATgtaagttggtcatttcccgttttgcttttgataacttagtttttcttacaatattttccaaacttaccagattcatttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT