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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacattgattatcatgcattgattgttttttcagtttgaattaggtctagttagttgaaatgaggtagttttaaggaaccatttatagtagaattttggaagtgagctgtgaggaaacagacattccaatagtctcagttttggactgagatacatcttgtgaatcttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAGCACTTTTCGCAGCGTCCTATCAAG

Basic information

species Arabidopsis thaliana
transcript AT3G23390.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
gtaacattgattatcatgcattgattgttttttcagtttgaattaggtctagttagttgaaatgaggtagttttaaggaaccatttatagtagaattttggaagtgagctgtgaggaaacagacattccaatagtctcagttttggactgagatacatcttgtgaatcttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAGCACTTTTCGCAGCGTCCTATCAAG
||||       |||| |   ||||||||  ||  |  ||       ||||  || | ||  |  | | |  | ||  |||  || |      ||||| |  | |   | || |||              |||| | |  | | || ||  |  |  ||  | | |||    ||  ||||| |||||||| |||||||||||| ||| ||| ||||| || |||||||||||||  || ||||   | ||||||
gtaatgcaacatatc-tat-ttgattgtacttataccttt------gtctgttttgatggtagcatgaatgtcta--gaaatatctgc----gaattctaaatgcctgttgagag--------------aataatttgggatatg-acaaatgtg-attgtattaataccttt--cagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG

upper sequence: AT3G23390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G125527_T02 (Zea mays), 3'ss of exon 2
gtaacattgattatcatgcattgattgttttttcagtttgaattaggtctagttagttgaaatgaggtagttttaaggaaccatttatagta-gaattttggaagtgagctgtgaggaaacagacattccaatagtctcagttttggactgagatacat---cttgtgaatcttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAGCACTTTTCGCAGCGTCCTATCAAG
                                      || |  |  |||| ||  ||| | | |     || |  |     ||   ||| | |||| |  |||   | ||| ||      | |         |||      | |||  |  || | ||    ||||   | |   |  ||||| |||||||| |||||||||||| ||| ||| ||||| || |||||||||||||  || ||||   | ||||||
----------------------------------gtaatgcagcatatctatttgattgtacttatacctttgtctgttttgatgc-tagcatgaatgtctgaaaatatctgcgaattc-taaatgcctgttcagtgattaatgtgggatatgacaaatgagattgtatttatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG

upper sequence: AT3G23390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0064g00880.t01 (Vitis vinifera), 3'ss of exon 2
gtaacattgattatcatgcattgattgttttttcagtttgaattaggtctagttagttgaaatgaggtagttttaaggaaccattt--atagtagaattttggaagtgagctgtgaggaaacagacattccaatagtctcagttttggactgagatacatcttgtgaatcttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAGCACTTTTCGCAGCGTCCTATCAAG
                                                                     | || |  | | | ||   || || |  || |  || | |      ||  ||  ||   |  |||  |||   |  | || |||   |  ||   ||   |||   |||||||||||||||| |||||||||||| ||||||| ||||| ||  | ||||| ||| | || ||||  || ||||||
---------------------------------------------------------------------ggttaactgtatccttagaattgttggcttctcaaattaactatcaagccaattgaggct--aat--tct---tcatagattgac-catttcccttgtgcctt---aacagGCTAAGACCACCAAGAAGATTGTTCTGAGGCTCCAGTGCCAGGGTTGCAAACACGTATCCCAGCACCCAATCAAG

upper sequence: AT3G23390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S115_63V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaacattgattatcatgcattgattgttttttcagtttgaattaggtctagttagttgaaatgaggtagttttaaggaaccatttatagtagaattttggaagtgagctgtgaggaaacagacattccaatagtctcagttttggactgagatacatcttgtgaatcttgttaa--cagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAGCACTTTTCGCAGCGTCCTATCAAG
          ||| | |   |   |||| | |   |  | |||  | | |   |  ||  | ||  |  |  |     || |   |  |||  |||  |  || |    | | |   |       |    ||| | |   |||| ||||   || | ||    |||||||||     ||||||||||||||||||||||||||  | ||| | || || ||   |||||||||| |  | || | ||||||||||
---------gttagcttaactctgttgtatgtcttggatcaatatgttgtgactcctttcagtg--gctgcct----aaatctcatgcagttaaatactttaacta---tttaatttagtgattgt----ata-tgttgctttttgact---atgc-tcaccagaatcttgtgcgtgcagGCTAAGACCACGAAGAAGATTGTGCTTAGGTTGCAATGCCAGGCCTGCAAGCACGTGACACAACATCCTATCAAG

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|124704277|gb|EH795679.1|EH795679
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACG
EST: gi|301501066|gb|HO206606.1|HO206606
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|164102331|gb|ES202464.1|ES202464
EST:     TAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAAG                         GCTAAGACCACGAAGAA
genomic: TAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAA-Ggtaacattga ... ttgttaacagGCTAAGACCACGAAGAA
EST: gi|86076372|gb|DR372129.1|DR372129
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|163967601|gb|ES138172.1|ES138172
EST:     CTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: CTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|125011355|gb|EL083624.1|EL083624
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAG
EST: gi|124726879|gb|EH818281.1|EH818281
EST:     TAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: TAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|47828759|gb|CK118443.1|CK118443
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|152035372|gb|BP851782.2|BP851782
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTC-ACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGAAAG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|124897663|gb|EH973877.1|EH973877
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GACTAAGACCACGAAGAAGATTGTTTTGAGGCT
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagG-CTAAGACCACGAAGAAGATTGTTTTGAGGCT
EST: gi|163973205|gb|ES012805.1|ES012805
EST:     CTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: CTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|125302671|gb|EL316756.1|EL316756
EST:     ACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTTGCAA
genomic: ACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCT-GCAA
EST: gi|124889994|gb|EH968896.1|EH968896
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCT
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCT
EST: gi|163996673|gb|ES146525.1|ES146525
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAA
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAA
EST: gi|164207487|gb|ES087398.1|ES087398
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|124837669|gb|EH922108.1|EH922108
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|164058645|gb|EL971029.1|EL971029
EST:     TAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAA
genomic: TAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCAC-AAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAA
EST: gi|86086549|gb|DR382308.1|DR382308
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCNCGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|124996583|gb|EL068852.1|EL068852
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATT
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATT
EST: gi|125132501|gb|EL174550.1|EL174550
EST:     GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCAC-AAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: GTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
EST: gi|125038750|gb|EL111019.1|EL111019
EST:     ATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTG
genomic: ATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTG
EST: gi|164095081|gb|ES173980.1|ES173980
EST:     TGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAG                         GCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG
genomic: TGGTTATGGTGGTCAGACTAAGCCTGTCTTCCACAAAAAGgtaacattga ... ttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattccaatagtctcagttttggactgagatacatcttgtgaatcttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAGCACTTTTCGCAGCGTCCTATCAAG
                                           tcttgtt  CT-rich tract
                                             ttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacattgattatcatgcattgattgttttttcagtttgaattaggtctagttagttgaaatgaggtagttttaaggaaccatttatagtagaattttggaagtgagctgtgaggaaacagacattccaatagtctcagttttggactgagatacatcttgtgaatcttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAGCACTTTTCGCAGCGTCCTATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC