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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactacttatactctcttgcaattgttgtatacttttaagtatattctgcttattagctgattgcattgagctgcttattttttttcttcgcttatattgcaaatggattcttattctttcaccattcattttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAAGAAGAAGCCTAAGAAAGGTTCAAAGAATACTAAACCAATCACCAAACTC

Basic information

species Arabidopsis thaliana
transcript AT4G26110.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26110.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g46230.1 (Oryza sativa), 3'ss of exon 7
gtaactacttatactctcttgcaattgttgtatacttttaagtatattctgcttattagctgattgcattgagctgcttattttttttcttcgcttatattgcaaatggattcttattctttcaccattc--attttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAAGAAGAAGCCTAAGAAAGGTTCAAAGAATACTAAACCAATCACCAAACTC
                                                 |   || ||  | |   | |  || |      ||  | | || | | |     ||  |  |     ||   |    |||||   ||||||| || |||||||| ||||  ||||| |||||| | || || ||| ||||||||||||| || ||||| || |||||||| |||||||| ||||| |||   
------------------------------------------------gtaactaatatttcaactcgtgaagtt------ttactcttttagatgaatggacagtttcaccaacatatctctgacattcttgttttcagTACTGAAATTGAATGGTTCCCTGGGAAGTGTTTGACACAAAAGGTTCTCAAGAAGAAACCAAAGAAGGGCTCAAAGAACACTAAACCTATCACAAAAACT

upper sequence: AT4G26110.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G16500.2 (Glycine max), 3'ss of exon 7
gtaactacttatactctcttgcaattgttgt-atacttttaagtatattctgcttattagctgattgcattgagctgcttattttttttcttcgcttatattgcaaatggattcttattctttcaccattcattttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAAGAAGAAGCCTAAGAAAGGTTCAAAGAATACTAAACCAATCACCAAACTC
||||   |||      | |||  ||| || | |||  | |||   ||     ||||       ||    |      | ||    | |   |      | ||||       ||| |  ||  ||      | | ||||||||| |||||| | ||| | || ||||| || || || ||||||||||| ||||| ||||||||||| |||||||||||| |||||||||| ||||||   
gtaa--gctttattgttgttgttattattattataaatgtaaccttaccacccttaacttactatcatgtcagaagggttggcgtatccttgaataaaaattgtttgctaattttattttatttttttataactttcagGACTGAAATTCAATGGCACCCAGGAAAATGCCTGACACAGAAGATTCTTAAGAAAAAGCCTAAGAAGGGTTCAAAGAATGCTAAACCAATTACCAAAACT

upper sequence: AT4G26110.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G07410.2 (Glycine max), 3'ss of exon 7
gtaactacttatactctcttgcaattgttgtatacttttaagtatattctgcttattagctgattgcattgagctgcttattttttttcttcgcttatattgcaaatggattcttattctttcaccattcattttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAAGAAGAAGCCTAAGAAAGGTTCAAAGAATACTAAACCAATCACCAAACTC
           ||  || ||    ||     || || |||  | || |||| ||   |  || |  || | |  |    |  || |  ||     |  |||     | ||||  |    |||     |||| |   ||||| |||||||| ||||| || ||||| ||| | ||||||||| || | ||||| ||||||||||| |||||||||||| |||||||||| ||||||  |
----------gtatgctgttcattttacctgatgctatta--tgtaatctgttt-ccatttgttcacaatcatgtcaaaaggttctggctcgatgttgattaaggtttgattgctgccttttttttgttcaat---agGACGGAAATTGAATGGTACCCGGGAAAATGTTTGACTCAGAAGGTTTTGAAGAAAAAGCCTAAGAAGGGTTCAAAGAATGCTAAACCAATTACCAAAACC

upper sequence: AT4G26110.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G18600.1 (Glycine max), 3'ss of exon 7
gtaactacttatactctcttgcaattgttgtatacttttaagtatattctgcttattagctgattgcattgagctgcttattttttttcttcgcttatattgcaaatggattcttattctttcaccattcatttt-cagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAAGAAGAAGCCTAAGAAAGGTTCAAAGAATACTAAACCAATCACCAAACTC
                         || |||  | |||  |  ||  | |   | | | ||| || |||||   |    ||  |  |     | |     |  |  | ||||    || | || |  ||  |||   ||||| |||||||| ||||| || ||||| ||  | ||||||||| || | ||||||||||||||||| |||||||||||| |||||||||| ||||||   
----------------------gtatggtgttcattttacatgatgctat-tatgtaatctgtttccattg--tttacaatcatgatgaaaaggtctggcttgatgttgattacggttttgtctctttttttttaatagGACGGAAATTGAATGGTACCCGGGAAAATGCTTGACTCAGAAGGTTTTGAAGAAGAAGCCTAAGAAGGGTTCAAAGAATGCTAAACCAATTACCAAAACT

upper sequence: AT4G26110.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G06170.5 (Glycine max), 3'ss of exon 8
-------------------------------------gtaactacttatactctc-ttgcaattgttgtat-acttttaagtatattctgcttattagctgattgcattgagctgcttattttttttcttcgcttatattgcaaatggattcttattctttcaccattcattttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAAGAAGAAGCCTAAGAAAGGTTCAAAGAATACTAAACCAATCACCAAACTC
                                     | || || |  || | |  ||  || ||||   | || | | |  |   | ||||      || ||    |      | ||   ||  |  |      | ||||      |||| ||    ||     |||   ||||||||| |||||| | ||| | || ||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||| |||||||||| ||||||   
gtaagctttattattgttattatgttttttttttgcgggaattattattattattattataagtgttaccttacctgttaccaccct-tgctagactact-atcatgtcagaagggttggcttagtcttgaataaagattgtttgctgattttttaatttcttttattt-ctttcagGACTGAAATTCAATGGCACCCAGGAAAATGTCTGACACAGAAGATTCTTAAGAAAAAACCTAAGAAGGGTTCGAAGAATGCTAAACCAATTACCAAAACT

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|47831827|gb|CK121511.1|CK121511
EST:     TCTTATCATATGATTGATGAAGATGAGCCACTGCTTGAGAAGGCTATGGG                         GACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAA
genomic: TCTTATCATATGATTGATGAAGATGAGCCACTGCTTGAGAAGGCTATGGGgtaactactt ... tcattttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAA
EST: gi|164130559|gb|ES046365.1|ES046365
EST:     TCTTATCATATGATTGATGAAGATGAGCCACTGCTTGAGAAGGCTATGGG                         GACAGAAATTGATTGGTATCC
genomic: TCTTATCATATGATTGATGAAGATGAGCCACTGCTTGAGAAGGCTATGGGgtaactactt ... tcattttcagGACAGAAATTGATTGGTATCC
EST: gi|124932559|gb|EL009806.1|EL009806
EST:     CCACTGCTTGAGAAGGCTATGGG                         GACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGNTTCTCAA
genomic: CCACTGCTTGAGAAGGCTATGGGgtaactactt ... tcattttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAA
EST: gi|164064261|gb|ES146856.1|ES146856
EST:     AAGGCTAT-GG                         GACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAA
genomic: AAGGCTATGGGgtaactactt ... tcattttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcttcgcttatattgcaaatggattcttattctttcaccattcattttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAAGAAGAAGCCTAAGAAAGGTTCAAAGAATACTAAACCAATCACCAAACTC
                                 ttctttcaccattc  CT-rich tract
                          attcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactacttatactctcttgcaattgttgtatacttttaagtatattctgcttattagctgattgcattgagctgcttattttttttcttcgcttatattgcaaatggattcttattctttcaccattcattttcagGACAGAAATTGATTGGTATCCTGGAAAGTGTCTAACTCAGAAGATTCTCAAGAAGAAGCCTAAGAAAGGTTCAAAGAATACTAAACCAATCACCAAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA