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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtttctttttttagttgcttcttgttttcatgatttagtactattgaattctgttgtgatctttgttttctctcttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCTTACTCAAGGTCGATTGTCGGTGCTACTTTGGAGGTTATTCAGAAGAAGC

Basic information

species Arabidopsis thaliana
transcript AT2G36620.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G36620.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G07680.1 (Glycine max), 3'ss of exon 3
------gtaatgtttctttttt-tagttgcttcttgttttcatgatttagtactattgaattctgttgtgatc-----tttgttttctctcttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCTTACTCAAGGTCGATTGTCGGTGCTACTTTGGAGGTTATTCAGAAGAAGC
      || ||   || | |    || ||  | |  |     | |||  | | | ||   ||   || | ||      ||||| |||     |  |  |||||   || ||||| |||||||||| ||| ||||||||  | || ||||||||||| ||||| ||||||||||| |||||||| ||||| ||||| ||| 
tacttggttattcctcatataaacaggtgactttgctacaagtaattctgcattgtttgcttgcattttaattgattgtttgtgttcatgtgttgtgtagGACATTGCTCAAGAAGCTGTGAAGAAAAGAAGACGTGCTGCCAAAAAGCCTTACTCCAGGTCCATTGTCGGTGCCACTTTGGAAGTTATCCAGAAAAAGA

upper sequence: AT2G36620.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G21520.1 (Glycine max), 3'ss of exon 3
--gtaatgtttctttttttagttgcttcttgttttcatgatttagta--ctat-------tgaattctgttgtgatc-tttgttttctctcttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCTTACTCAAGGTCGATTGTCGGTGCTACTTTGGAGGTTATTCAGAAGAAGC
   |  |  ||| |    ||    |||     |   || | | | ||  | ||       || ||| |  | ||||  ||||| | |        || ||||    || ||||| ||||||||||  || |||||||| || || || |||||||| ||||| ||||| ||||||||||| || ||||| ||||| ||| 
acttggttattcctcacataaacacttgactgtgctataagtaaatatccaatggttgcatgcattttaatttgattgtttgtgtgcatgtgatgtatagGATATTGCTCAAGAAGCTGTGAAGAAGAGAAGACGTGCTACCAAAAAACCTTACTCTAGGTCTATTGTTGGTGCTACTTTAGAAGTTATCCAGAAAAAGA

upper sequence: AT2G36620.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 3
gtaatgtttctttttttagttgcttcttgtttt-catgatttagtactattg-aat-----------tctgttgtgatc-tttgttttctctcttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCTTACTCAAGGTCGATTGTCGGTGCTACTTTGGAGGTTATTCAGAAGAAGC
  | || || ||| | |   ||     |||    |||   |||||| || || |||           | ||   ||||  ||||| | |        |  |||||   || ||||| ||||||||||  |||||||| ||  | || ||||||||||| ||||| ||||| ||||| ||| |||| ||||| ||||| ||| 
--attggttgtttgtgtgcatgtcatgtgtaggacattgcttagtaatactgcaatggttgcatgcatttgaattgattgtttgtgtgcatgtcatgtgtagGACATTGCTCAAGAAGCTGTGAAGAAGAGGAGACGCGCTGCCAAAAAGCCTTACTCTAGGTCCATTGTTGGTGCCACTCTGGAAGTTATCCAGAAAAAGA

upper sequence: AT2G36620.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgtttcttt-ttttagttgcttcttgttttcatg-atttagtactattgaattctgttgtga--tctttgttttc--tctcttctta----------cagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCTTACTCAAGGTCGATTGTCGGTGCTACTTTGGAGGTTATTCAGAAGAAGC
    ||| | | | |||| ||  |||  ||         ||  | ||    | |  | ||||| ||  | ||||||||   || ||  ||           |||||    || ||||||||||| ||||  ||| | ||||| || || ||||| ||||| ||||| ||||| |||||||| ||||||||||| |||||||   
----tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtttgttgggagttatttgttttgagtcactaattgggttaatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA

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|164015981|gb|ES169592.1|ES169592
EST:     TAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
genomic: TAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
EST: gi|164152551|gb|ES035585.1|ES035585
EST:     AGCCATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGG
genomic: AGCCATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGG
EST: gi|164155561|gb|ES149773.1|ES149773
EST:     CTGCTATGT-CCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
genomic: CTGCTATGTACCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
EST: gi|164077186|gb|ES098768.1|ES098768
EST:     GCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAAGAGACGTGCAACTAAGAAGCCT
genomic: GCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
EST: gi|125017702|gb|EL089971.1|EL089971
EST:     TTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
genomic: TTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
EST: gi|125288955|gb|EL303040.1|EL303040
EST:     AGCCATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTTGTGAAGAGAAGGAGACGT
genomic: AGCCATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCT-GTGAAGAGAAGGAGACGT
EST: gi|47829129|gb|CK118813.1|CK118813
EST:     AGCCATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
genomic: AGCCATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
EST: gi|124793371|gb|EH883050.1|EH883050
EST:     CCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
genomic: CCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
EST: gi|125011840|gb|EL084109.1|EL084109
EST:     TGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
genomic: TGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
EST: gi|124737372|gb|EH828774.1|EH828774
EST:     AGCCATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGA
genomic: AGCCATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGA
EST: gi|124719092|gb|EH810494.1|EH810494
EST:     CAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
genomic: CAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
EST: gi|164035217|gb|ES155995.1|ES155995
EST:     AAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
genomic: AAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCT
EST: gi|164179525|gb|ES088095.1|ES088095
EST:     CATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAG                         GACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAG
genomic: CATCTAAGCTTTGCTGGACTGCTATGTACCGAAAGCAGCACAAGAAGgtaatgtttc ... cttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgatttagtactattgaattctgttgtgatctttgttttctctcttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCTTACTCAAGGTCGATTGTCGGTGCTACTTTGGAGGTTATTCAGAAGAAGC
                               tctttgttttctctct  CT-rich tract
             tattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtttctttttttagttgcttcttgttttcatgatttagtactattgaattctgttgtgatctttgttttctctcttcttacagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCTTACTCAAGGTCGATTGTCGGTGCTACTTTGGAGGTTATTCAGAAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC