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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaaaatccaactgatcccgtctttaagctatccacataaaccatagtttcctaaatatcatctcatattctgatggttgttgcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT

Basic information

species Arabidopsis thaliana
transcript AT3G26935.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
-gtaagtcaaaatccaactgatcccgtctttaagctatccacataaaccatagtttcctaaatat----catctca--tattctgatggttgtt---gcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT
  |     ||||| |   | |       | ||   | | |  ||   ||||  ||   ||   ||    ||||  |  |  |  |||  || ||   |||| | || || || |||||||||||||| |||||||| || || || |||||||||||||| ||||| || ||||||||||| ||   ||  ||||||| ||
aatggaggaaaattctgtttacttttcatctatcatttgc-tatgtgccatccttgaatatgcattatgcatcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT

upper sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G05670.2 (Glycine max), 3'ss of exon 3
gtaagtcaaaatccaactgatcccgtctttaagctatccac----ataaaccatagtttcctaaatatcat-----ctcatattctg-atggttgtt--gcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT
   | |     |     |         ||| || ||||       ||  |  ||  ||   || | || ||     || ||    || | | || ||  |||| | || || || |||||||||||||| |||||||| || || || || ||||||||||| ||||| || ||||||||||||||   ||  ||||||| ||
---attattttttttgttctgtttacttttcagttatcatttgctatgcattattattgaatatacattatgtatcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTGTGTATATATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGCAT

upper sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 3
---gtaagtcaaaatccaactgatcccgtctttaagctatccacataaaccatagt-ttcctaaatatcatctc-----atattctgatggttgtt--gcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT
   |||  |  |  ||    |         ||| || |||  |  | |  |||     || | ||| | || |      || |    |   |||||  |||| | || || || |||||||||||||| |||||||| || || || || ||||||||||| || || || || ||||||||||| ||||  ||||||||  
attgtatatatatttctggtttggtg-acttttcagttatt-atttgatacatgtcactcttgaatgttatgtatctgaatgtgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG

upper sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 3
gtaagtcaaaatccaactgatcccgt---ctttaagctatccacataaaccatagtttcctaaatatcatct---catattctg-atggttgtt--gcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT
    ||  | ||    ||| |   ||    ||| || |||     || ||      ||| | ||| | || |      ||| || |   |||||  |||| | || || || |||||||||||||| |||||||| || || || || ||||||||||| || || || || ||||||||||| ||||  ||||||||  
aattgtatatatatttctggtttggtgacttttcagttattattttatacatgtcattcttgaatgttatgtatctgaattgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG

upper sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 3
---gtaagtcaaaatcca-actgatcccgtctttaagct--atccacataaaccatagtttcctaaatatcatctcatattctgatggttgt---tgcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT
      |||    |||   ||  |     |    | | |  ||   | | ||     |     |  ||        | | | | |   || |   ||||| | || || ||||| ||||||||||| |||||||| ||||| ||||| ||||||||||||||||  ||||||||||||||||| |  | ||| ||||| |
ttttccagttgtcatcttcaccaacatgataggaatgatgcatgtgcttgaatttgtgggcaatgcatgaatctgaacactttcacaattctgggtgcagCGTAATTATCGATTTTTCTTCATGTTTGTCTTCTCGACGACTCTTCTTTGTATATATGTGTTTGGGTTCTGCTGGGTCTATATTAAGAGGATCATGGATT

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|164090159|gb|EL983656.1|EL983656
EST:     TAGAAAGGTTTGACCATCACTGCCCTTGGGTCGGCCAATGTATTGGGATG                         AGGAACTACCG
genomic: TAGAAAGGTTTGACCATCACTGCCCTTGGGTCGGCCAATGTATTGGGATGgtaagtcaaa ... gttgttgcagAGGAACTACCG
EST: gi|125277136|gb|EL291221.1|EL291221
EST:     TAGAAAGGTTTGACCATCACTGCCCTTGGGTCGGCCAACGTATTGGGATG                         AGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCT
genomic: TAGAAAGGTTTGACCATCACTGCCCTTGGGTCGGCCAATGTATTGGGATGgtaagtcaaa ... gttgttgcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCT
EST: gi|124796573|gb|EH886252.1|EH886252
EST:     TAGAAAGGTTTGACCATCACTGCCCTTGGGTCGGCCAATGTATTGGGATG                         AGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTA
genomic: TAGAAAGGTTTGACCATCACTGCCCTTGGGTCGGCCAATGTATTGGGATGgtaagtcaaa ... gttgttgcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacataaaccatagtttcctaaatatcatctcatattctgatggttgttgcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT
                     taaatatcat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaaaatccaactgatcccgtctttaagctatccacataaaccatagtttcctaaatatcatctcatattctgatggttgttgcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA