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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatacagtcttgattcaaatgtgaacaattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG

Basic information

species Arabidopsis thaliana
transcript AT3G10090.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G124143_T03 (Zea mays), 3'ss of exon 1
----tatacagtcttgattcaaatgtgaacaattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG
    |   |||| |  | |  || |     | ||       | |  | |     |      |  |  |  |||    ||||    |  | || |       ||| |||||  | ||  | ||||  |||||||| ||||| |||||||||||||| || || |||||||| || || ||||| ||||||||||||   ||    
ttgtttgccagtttctacttcaaagctgtgatttgaggaactttgtgaaca---aagggcctgattcaccttgacaactgacaaatgct-ttctacaagtgcagTATGGACACCCAAGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGAAGGACCGGCTCCAGGGGTCAGGTTACCCAGGTCAGAGTGAAGTTCTTGGATGAC

upper sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G455828_T01 (Zea mays), 3'ss of exon 1
tatacagtcttgattcaaatgtgaa--caattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG
     ||     |  ||  ||  |   || ||    |   ||| |   |   |    | | ||  |  ||| |  ||||    |  | || | || |  ||| |||||  | ||| | ||||  |||||||| ||||| |||||||| ||||| || || |||||||| ||||| ||||| |||||||||||    ||    
ccagtagcaacaaaccatgtgacagtgcagttaaaatgaactatgtgatcaaagca-tatggttcaccttgattactgacaaatgct-ttctattaatgcagCATGGACACCCAGGTGAAGCTTGCTGTTGTGGTGAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTTTTGGATGAC

upper sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G030293_T02 (Zea mays), 3'ss of exon 1
tatacagtcttgattcaaatgtgaa--caattctctttttctaaggattttcacttcttttgtaaaatt--tggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG
   | |||    | |||  ||  |   || ||    |   | | |       |     |   | |  ||  |    | | |||| |||     |||  |  ||| |||||  | ||  | ||||  |||||||| || || |||||||| ||||| || || |||||||| ||||| ||||| ||||||||||||   ||    
ccaatagtaccaaatcatgtgacagtgcagttgaaatgaaccatgcgaacaaagcaaatgattcaccttgataacttataaatgctttc----tgtcaatgcagCATGGACACCCAAGTGAAGCTTGCTGTTGTGGTAAAGGTGATGGGCAGGACCGGCTCCAGGGGTCAGGTGACCCAGGTCAGAGTGAAGTTCTTGGATGAC

upper sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G36420.1 (Glycine max), 3'ss of exon 1
tatacagtcttgattcaaatgtga--acaattctctttttctaaggatttt--cacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG
     | || ||||| |  |||||     | |   |   | | | |  ||   | |   | || |  | |||  ||||  ||  | ||  || ||||  ||||| ||||| |||||| | ||||| ||| |||| || ||||| |||||  | |||||||| || || || |||||||||||||||||||||||    ||    
---ttattcctgatttatctgtgatgctgactgattaactgtgatgcattaaacgcaattgttttccactttcatctcataac-tgttgattgtgtttgatcagGATGGAGTCTCAGGTGAAGCATGCTCTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT

upper sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G39070.1 (Glycine max), 3'ss of exon 1
--tatacagtcttgatt-caaatgtgaacaattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG
   |||||   ||   |   |  |||| |||||  || |     |  |    || || ||||  | | |    ||    ||  | ||  || ||||  | ||| ||||| |||||| | ||||||||  |||| || ||||| |||||  | |||||||| || || |||||||| |||||||||||||||||    ||    
gtgatacatatttacctgtcacggtgaccaattagctgtgatgcattaaacccaattgttttccacattcatctcataaaaactgttgattgtgtttgagCAGGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTTATGGGTCGTACTGGATCCAGAGGACAAGTGACCCAGGTTAGAGTGAAGTTTTTGGAT---

upper sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G37600.1 (Glycine max), 3'ss of exon 2
----------tatacagtcttg--attcaaatgtgaacaattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG
          || ||  |  ||   | ||||||  |  ||  |  | ||    |  ||  | ||| |  ||  || |||       |||||| |||     ||||  | ||| ||||| |||||| | ||||||||  |||| || ||||| |||||  | ||||| || ||||| || |||||||||||||||||||||||    ||    
tatgttgccctacacttttctgttgtccaaatggaatgaaagcaatgttgtccacaatccttactccactt--aacatta------tgaatgctttg----tgtttgagcagGATGGAATCTCAGGTGAAGCACGCCCTTGTTGTCAAAGTTATGGGTCGTACTGGGTCTAGGGGGCAGGTGACTCAGGTTAGAGTGAAGTTTTTGGATGAT

upper sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G36580.1 (Glycine max), 3'ss of exon 1
tatacagtcttgattcaaatgtgaacaattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG-
|  |       |||   | |    |    ||| |  ||       |   ||| | | || |  | |||  ||||  || | |||  || ||||  | ||| ||||| |||||| | ||||||||  |||| || ||||| |||||  | |||||||| || || || ||||| |||||||||||||||||  |||  |   
tgcatttggaagatgttattcctgatttatctgtcattgattcattaaacacatttgttttccactttcatctcataacggtttgattgtgtttgagcagGATGGAGTCTCAGGTGAAGCACGCACTTGTTGTCAAAGTAATGGGTCGTACTGGATCCAGAGGACAGGTGACCCAGGTTAGAGTGAAGTTT-CTGGATGAT

upper sequence: AT3G10090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g07210.t01 (Vitis vinifera), 3'ss of exon 1
--tatacagtcttgattcaaatgtgaac---aattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG
  |       |||   |  ||  ||||    ||  |   ||   | |  | |    |||  | | ||  | ||     | | |  ||| | |          |  ||||||| |   | | ||||| ||||| || |||||||| |||||  | ||||||||||||||||| ||||| ||||| |||||||||||    |     
aatgagtttgcttttatagaacttgaaaggaaaaaccaattaaatgaaaaatggtgcttagtatttatgaattataaccagcaattttctttggcagcagTGCGAAATGGATGCCGGGGTGAAGCATGCTGTGGTGGTGAAAGTTATGGGTCGAACTGGATCAAGGGGTCAGGTGACACAGGTGAGAGTGAAGTTTTTGG-----

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|19742407|gb|AU227760.1|AU227760
EST:     AACTCTTATCCCCGCTAAAACTCTCTACCCATCGCAGAGCCTCTCTAAAG                         AATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAG-AC
genomic: AACTCTTATCGCCGCTAAAACTCTCTACCCATCGCAGAGCCTCTCTAAAGgttatcttca ... gttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGAC
EST: gi|86067321|gb|DR363078.1|DR363078
EST:     AACTCTTATCGCCGCTAAAACTCTCTACCCATCGCAGAGCCTCTCTAAAG                         AATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGNGAAGGAC
genomic: AACTCTTATCGCCGCTAAAACTCTCTACCCATCGCAGAGCCTCTCTAAAGgttatcttca ... gttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGAC
EST: gi|125060607|gb|EL129284.1|EL129284
EST:     AGCCTCTCTAAAG                         AATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGAC
genomic: AGCCTCTCTAAAGgttatcttca ... gttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG
                                         ttttgtt  CT-rich tract
       ttcttttgtaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatacagtcttgattcaaatgtgaacaattctctttttctaaggattttcacttcttttgtaaaatttggtctctgaatgtttttgttttgttgaatcagAATGGATTCTCAGATCAAGCACGCTGTTGTAGTGAAAGTGATGGGAAGGACTGGATCAAGGGGTCAAGTGACTCAGGTTAGAGTGAAGTTCACTGACTCG

- - - - - - attcaaa
- - - - - - - - - - - gaacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttttg