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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgatgtcgaaaaccctagttttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagttgtgtagaccaatgcatttgttgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC

Basic information

species Arabidopsis thaliana
transcript AT3G22110.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G22110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G43710.2 (Glycine max), 3'ss of exon 1
tgtgatgtcgaaaaccctagttttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagttgtgtagaccaatgcatttgttgtggtgcagGTGTTAA--AGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC---------------------
                     ||||   |||       ||  |||  |    ||    |||  |||  |    |   |   ||  |  ||||   |  |       |  |  |||||||| ||||||||||||||||| ||||||||||| || ||||| ||||||||||| || || |||||||||||||||||||| ||                      
---------------------tttctcatttattttctttttcctaagct--atactttattcattcctctcctttccttctgtttgcgttggactaaaaactcagatcaatatgtctcgaagATATGATAGCCGTACTACAATCTTCTCCCCTGAAGGACGTCTTTACCAAGTGGAATATGCTATGGAGGCCATTGGGAATGCTGGTACTGCAATAGGGATC

upper sequence: AT3G22110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G43710.1 (Glycine max), 3'ss of exon 1
tgtgatgtcgaaaaccctagttttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagttgtgtagaccaatgcatttgttgtggtgcagGTGTTAA--AGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC----
  |  | | | |   |||   ||||   |||       ||  |||  |    ||    |||  |||  |    |   |   ||  |  ||||   |  |       |  |  |||||||| ||||||||||||||||| ||||||||||| || ||||| ||||||||||| || || |||||||||||||||||||| ||     
-cttctataggagtgcct---tttctcatttattttctttttcctaagct--atactttattcattcctctcctttccttctgtttgcgttggactaaaaactcagATCAATATGTCTCGAAGATATGATAGCCGTACTACAATCTTCTCCCCTGAAGGACGTCTTTACCAAGTGGAATATGCTATGGAGGCCATTGGGAATGCTG

upper sequence: AT3G22110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G19170.1 (Glycine max), 3'ss of exon 1
tgtgatgtcgaaaaccctagttttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagttgtgtagaccaatgcatttgttgtggtgcagGTGTTAA--AGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC----
  |  | | | |   |||  ||||| | | ||      ||  |||  |    ||    |||  |||  |    |   |   ||  |   |||   |  |       |  |  |||||| | ||||||||||||||||| ||||||||||| || ||||| ||||||||||| || |||||||| |||||||||||||| ||     
-cttctataggagtgcctt-ttttcatttattttc--tttttcctaagct--atactttattcatttctctcctttccttgtgtttgctttgaactaaaaactcagATCAATATGTCTAGAAGATATGATAGCCGTACAACAATCTTCTCCCCCGAAGGACGTCTTTACCAAGTGGAGTATGCAATGGAGGCCATTGGGAATGCTG

upper sequence: AT3G22110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G19170.2 (Glycine max), 3'ss of exon 1
tgtgatgtcgaaaaccctagttttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagttgtgtagaccaatgcatttgttgtggtgcagGTGTTAA--AGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC---------------------
                     |||    |||       ||  |||  |    ||    |||  |||  |    |   |   ||  |   |||   |  |       |  |  |||||| | ||||||||||||||||| ||||||||||| || ||||| ||||||||||| || |||||||| |||||||||||||| ||                      
---------------------tttttcatttattttctttttcctaagct--atactttattcatttctctcctttccttgtgtttgctttgaactaaaaactcagatcaatatgtctagaagATATGATAGCCGTACAACAATCTTCTCCCCCGAAGGACGTCTTTACCAAGTGGAGTATGCAATGGAGGCCATTGGGAATGCTGGAACTGCAATAGGGATC

upper sequence: AT3G22110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G31360.3 (Glycine max), 3'ss of exon 1
tgtgatgtcgaaaaccctagt-tttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagttgtgtagaccaatgcatttgttgtggtgcagGTGTTAAAGA-----ATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC
     | |   ||     | | |||| |  |||  | |     |  |    ||   |  ||     |  |  | |  | |     | ||    | |  |||   | | |||     |||||||| |||||||| |||||||| ||||||||||| || ||||| ||||||||||| || || ||||| |||||||| ||||     
aaaagtattagaattttaattctttcctcctttttgcatcaaactaggaaatacctgtttaattcctt-tcatttccatcttgctactttgcatagatcagTAATCAGAGATCAAAATGTCTCGAAGATATGACAGCCGTACAACAATCTTCTCCCCGGAAGGACGTCTTTACCAAGTGGAATATGCAATGGAGGCTATTG-----

upper sequence: AT3G22110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G06350.2 (Glycine max), 3'ss of exon 1
tgtgatgtcgaaaaccctagttttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagtt--gtgtagaccaatgc-atttgttgtggtgcagGTGTTAAAGA-----ATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC
     | |   ||     | | ||  | |  |     | | |   ||    |||      | ||||  ||   | |  |    ||| | || |  | |  |||  || | |||     |||||||| |||||||| |||||||| ||||||||||| || ||||| ||||||||||| || || ||||| |||||||| ||||     
--aagtattagaattttaattctttctctcctttttgcat-caaagtaggaaatacctgtttaatttctttcattttcatttttgctacttttcatagatcagTAGTCAGAGATCAAAATGTCTCGAAGATATGACAGCCGTACAACAATCTTCTCCCCTGAAGGACGTCTTTACCAAGTGGAATATGCAATGGAGGCTATTG-----

upper sequence: AT3G22110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G31360.2 (Glycine max), 3'ss of exon 1
-----tgtgatgtcgaaaaccctagt-tttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagttgtgtagaccaatgcatttgttgtggtgcagGTGTTAAAGA-----ATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC
          | |   ||     | | |||| |  |||  | |     |  |    ||   |  ||     |  |  | |  | |     | ||    | |  |||   | | |||     |||||||| |||||||| |||||||| ||||||||||| || ||||| ||||||||||| || || ||||| ||||||||          
gaaaaaaaagtattagaattttaattctttcctcctttttgcatcaaactaggaaatacctgtttaattcctt-tcatttccatcttgctactttgcatagATCAGTAATCAGAGATCAAAATGTCTCGAAGATATGACAGCCGTACAACAATCTTCTCCCCGGAAGGACGTCTTTACCAAGTGGAATATGCAATGGAGGC----------

upper sequence: AT3G22110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G06350.1 (Glycine max), 3'ss of exon 1
---tgtgatgtcgaaaaccctagttttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagtt--gtgtagaccaatgc-atttgttgtggtgcagGTGTTAAAGA-----ATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC
        | |   ||     | | ||  | |  |     | | |   ||    |||      | ||||  ||   | |  |    ||| | || |  | |  |||  || | |||     |||||||| |||||||| |||||||| ||||||||||| || ||||| ||||||||||| || || ||||| ||||||||          
gaaaaaagtattagaattttaattctttctctcctttttgcat-caaagtaggaaatacctgtttaatttctttcattttcatttttgctacttttcatagATCAGTAGTCAGAGATCAAAATGTCTCGAAGATATGACAGCCGTACAACAATCTTCTCCCCTGAAGGACGTCTTTACCAAGTGGAATATGCAATGGAGGC----------

upper sequence: AT3G22110.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv10s0042g00070.t01 (Vitis vinifera), 3'ss of exon 1
----------tgtgatgtcgaaaaccctagttt--tcgtgttttcggaacttgccctgtgt-ctaatggagt-atgaattagttgt-gtagacc-aatgcatttgttgtggtgcagGTGT--TAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC
          | || | | |||   | ||  |   | ||  ||        | || | ||  || ||    |    | |   |||| |||  |   |   | || ||  | | |  ||||  || | |||||||||||| |||||||||||||| |||||||| || || ||||| ||||| ||||| || ||||||||                   
ctcatttgtctctgtttttgaatttcatatctaagttgtacttctttcttgtaccttctgagctgataactttgctattccattgttgtactcttgacagACTTATTTCGTTTCCAGTGTGATACAAAATGTCTCGGAGGTATGATAGCCGTACAACAATCTTTTCCCCTGAAGGGCGTCTCTACCAAGTCGAGTATGCA------------------

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|86015468|gb|DR311214.1|DR311214
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|301501652|gb|HO207192.1|HO207192
EST:     GAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: GAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015476|gb|DR311222.1|DR311222
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015458|gb|DR311204.1|DR311204
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015465|gb|DR311211.1|DR311211
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|124940527|gb|EL016971.1|EL016971
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAA
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAA
EST: gi|86015461|gb|DR311207.1|DR311207
EST:     AAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015467|gb|DR311213.1|DR311213
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015462|gb|DR311208.1|DR311208
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015471|gb|DR311217.1|DR311217
EST:     AAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|116468504|gb|EG511096.1|EG511096
EST:     AAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015472|gb|DR311218.1|DR311218
EST:     CAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: CAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015473|gb|DR311219.1|DR311219
EST:     AAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015456|gb|DR311202.1|DR311202
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015474|gb|DR311220.1|DR311220
EST:     AAAGAAGAACCGAACGAGAGAGAGAAACAAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCDACAATCTTCTCGC
genomic: AAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACC-ACAATCTTCTCGC
EST: gi|86015460|gb|DR311206.1|DR311206
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015459|gb|DR311205.1|DR311205
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015470|gb|DR311216.1|DR311216
EST:     AAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015464|gb|DR311210.1|DR311210
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015466|gb|DR311212.1|DR311212
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
EST: gi|86015475|gb|DR311221.1|DR311221
EST:     AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAG                         GTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC
genomic: AGCAAAATCAAAGAAGAACCGAACGAGAGAGAGAAACGAATTCTTCTCAGgtattctctt ... tgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctaatggagtatgaattagttgtgtagaccaatgcatttgttgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC
  gtctaat  putative branch site (score: 3)
             tatgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgatgtcgaaaaccctagttttcgtgttttcggaacttgccctgtgtctaatggagtatgaattagttgtgtagaccaatgcatttgttgtggtgcagGTGTTAAAGAATGTCTCGGAGATATGATAGCCGTACCACAATCTTCTCGCCAGAAGGTCGTCTTTACCAGGTAGAGTATGCTATGGAGGCCATTGGAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - cgaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaccaa