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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaagacagaactcttaatgatttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT

Basic information

species Arabidopsis thaliana
transcript AT3G05530.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 9
-gtaaa--aaagacagaactcttaatgat-ttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtg--ttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT
 | ||   || | || | || |  |   | || |  ||| | |     |   |  ||||| || |    |     || |      |  | |||||     | |||||||||||||| ||||| |||||||| |||||||||||||| || |||||||||||||||||||| || || || |   | |||      |  |   |  
tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaac---atgaatctgtctgcttat--gtgaaaaattattaagaatgatttttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 6
gtaaa--aaagacagaactcttaatgatttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT
| ||   || | || | || |  |  || | ||  ||   | | || | | ||     ||   | |       ||   | |  || | | |     | |||||||||||||| |||||  ||||||| |||||||||||||| || |||||||||||||||||| | || || || |                        
gcaattcaatgccaaagctttggaccatgttagaatttgtaatatg-aatgtgtctgcttacgtgaaaaatcattaagtatgattttttgtccaattgcagGTGAACCATGAGGACTTTGATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGGATTATTATGCATAG----------------------

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 9
--gtaaaaaa-gacagaactct-taatgatttgagctttatgattgtgtagtttggtctgttttttaa-ggtggggttctctgttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCAT-TTATT
  ||   ||  | || | |||   |   | ||    ||| |  ||||||| |||      | ||  || | | |     |||||| |||| |      ||  ||||||||||||| ||||| ||||||||||| || |||||||| || ||||||||||||||| | || || || || |   ||   | |   | ||   ||| 
cagtgtcaattgtcaaagctccacaccaacttataatttgtt-ttgtgtattttacctgatgttggaatgttcgtaaaatctgtttttgt-tccaaacgt--agGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGCCTCAATTATTATGCATAGGCTGGATTTTGGAACAAGCTAT-

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 9
---gtaaaaaagacagaactcttaat-gatttgagctttatgattgtgtagtttggtctgttttttaa-ggtggggttctctgttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCT-CTCTCTCATCATTTATT
    |   |   ||| |||||   |   | |||   ||| |  || | || |||      | ||  || | | | |   |||||| |||| |      ||  |||||||||| || || || ||||||||||| || |||||||| || ||||||||||||||  ||||||| || || |   ||    | |   |  |  ||| 
ttcttttcagtaacaaaactccagaccaacttgtaatttgtt-ttatatattttacctgatgttggaatgttcgtgaaatctgtttttgt-tccaaacgt--agGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGTCTGAACTATTATGCATAGGCTGGATTGTGGAACAAGCTAT-

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
gtaaaaaagacagaactct-taatgatttga-gctttatga----ttgtgtagtttggtctgttttttaaggtggggttctct----gttgttgtgtttgtgtg--ttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT
           |||  ||| | ||| ||| | |   ||| |    |||     ||||  || |    |  |     || ||        |||    || || ||  | |||||||||||||| |||||||| |||||||| || ||||| ||||||||||||||| ||||||| || || || || |   ||    |||  | ||| |  |
-----------agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 9
gtaaaaaagacagaactcttaatgatttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctct-gttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT
                                           |||    |    ||  |  ||      | | | | | | |          |   ||||| |  || || |||||||| || || ||||||||||| || ||||||||||| || ||||||||||||||||| ||| |      |   |    |    
-------------------------------------------gtaa--cgacgcgtgatcgaatacacagctttttcgatctcactcgctctttcacagGTTACGCACGAGGACTTCAACGATGGCATCATCCAAGTGCAAGCCAAGAAGAAGGCCAGCTTGAACTACTACGCATGAGCAAATCATAGAAGGGATAGAA

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 9
gtaaaaaagacagaactcttaatgatttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctct-gttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT
                                           |||    |    ||  |  ||      | | | | | | |          |   ||||| |  || || |||||||| || || ||||||||||| || ||||||||||| || ||||||||||||||||| |||                      
-------------------------------------------gtaa--cgacgcgtgatcgaatacacagctttttcgatctcactcgctctttcacagGTTACGCACGAGGACTTCAACGATGGCATCATCCAAGTGCAAGCCAAGAAGAAGGCCAGCTTGAACTACTACGCATGA----------------------

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|164233584|gb|ES108850.1|ES108850
EST:     CAGTGTGTGTAGAGGCTGGCATGTTAGCTCTTCGCCGTGATGCCACAGAG                         GTGAACCATGAAGACTTCAA
genomic: CAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaaga ... gtgtgttcagGTGAACCATGAAGACTTCAA
EST: gi|124918842|gb|EH992643.1|EH992643
EST:     CAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAG                         GTGAACCATGAAG
genomic: CAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaaga ... gtgtgttcagGTGAACCATGAAG
EST: gi|124837257|gb|EH921696.1|EH921696
EST:     TGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAG                         GTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGG
genomic: TGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaaga ... gtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGG
EST: gi|125216401|gb|EL230484.1|EL230484
EST:     TAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAG                         GTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAG
genomic: TAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaaga ... gtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT
          tgttttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaagacagaactcttaatgatttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT