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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG

Basic information

species Arabidopsis thaliana
transcript AT1G23190.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 12
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
|||  | | |       ||    |  ||  |  |||||      |   | ||    || ||||||       ||| || || |||||| || || || ||||| |||||||| ||  ||||||||||||| ||||| ||  ||||||| |||||||| ||||| ||||
gtaagtattag-----gaccgtcagtcacatgattttcaaaatgccggacaagc--atatcatatga-----aaaccatatttcagGTGCCTACTGGGTGGAAATTTTTTGGGAACTTGATGGATGCTGGAATGTGCTCAATTTGTGGTGAAGAAAGCTTTGGCACTG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 12
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
     |   |   |  ||  |   |   ||    ||| |       | ||||    || | | ||    |  ||| ||  | |||||| || || || |||||||||||||| ||| ||||||||||||| ||||| ||  | ||||| |||||||| ||||| ||||
----gtaaaatattaaaatcttggttt-gcaagatttttgaatgtcatataa----atctgacata---aaaaaaccatgtttcagGTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
              | ||  | | |    | |   ||  |   | |    |   ||  |  || |  |    ||| ||  | |||||| || || || ||||| |||||||| ||| ||||||||||||| ||||| ||  | ||||| |||||||| ||||| ||||
--------------gtaaagtat-taagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 12
gtaca-tgtcaccgtgcaacttc---tatccagcttcttttctcctaactacata-atttaatttcatatctctattaa-atcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
||| | ||  |      |  ||     ||  |  | |||     | |  |  | | || |||||   ||  |  ||||  ||   | | ||||| || || || |||||||| ||||||||| | |||||||||||  | ||||| || ||||| |||||||||||||| ||||
gtatactgctattcaatatttttaagcatgaaaatacttgatggcgacttttagacatgtaattatttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 12
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataattta---atttcatatctctattaaatcac------atatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
    || |  |  | |||  ||| |  ||  |       | |    |     ||||   ||   ||   | |||| |||         | | ||||| || || || |||||||| ||||||||| | |||||||||||  | ||||| || ||||| |||||||||||||| ||||
--gtatattgctcttcaatgtcttttaagtatgaaaatacttgttgatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 6
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
                                                 |||||  |||| || |   | |||  |   | | ||||| || || || |||||||| ||||||||| | ||||||||| |  | ||||| || ||||| |||||||||||||| ||||
------------------------------------------------gtaatt--attttatttgattgtta--ttcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
-----gtacatgtcaccgtgc-aacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
      |   |  ||   |   |  |||| |   || || | |  |  | |||    |   |      | |   |      ||| ||  ||||| ||||| |||||||| |||||||||||  | |||||||||||  | |||||  ||||||| |||||||||||||||||||
gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatgagaggcatacatttgttattgactgttca-atgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S4_12V6.3 (Physcomitrella patens), 3'ss of exon 13
--------------------------------------------------------------------------gtacatgtcaccgtgcaacttctat--ccagcttctttt--------ctcctaactacataattta---atttcatatctctat-------taaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
                                                                           | | | |||  |||  |||   |   |||   ||||||        |||||  |||     |||    ||  | | | ||| |         ||   |||| ||||| |||||||| |||||||| |||||||| || ||||| || || ||||| || || || || ||||| ||||||||||| |
gttggttacactggttgagttgtaataatgactatttaagatatccaaaactacggcatagtctagttctctatattcgtttcattgtgacactagaagtgccatactcttttatcacttgctcctgcctattcgctttgctcatgacgtgtgtctgtacccggccgaaatccataccagGTACCAACAGGATGGAAGTTCTTTGGTAACCTCATGGACGCAGGCATGTGCTCGGTGTGCGGTGAAGAGAGTTTTGGAACAG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S168_70V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------------------------gtacatgtcaccgtgcaacttctatccagc--ttcttttctcctaac---tacataatttaatttcatatctcta-ttaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
                                                     ||   | || |  |||    | | | |     |  | |||||   |      ||| |  | | ||  | | | |   | ||   |    ||||| |||||||| |||||||| |||||||| || |||||||| || ||||| ||||| || || ||||| ||||||||||| |
gttggttcagcgtcttgaattggtgcatttaggaaatccaggattactgcagcgtggttctcgcactgctgtgtttgttccctcatcgtattctcgcgaggtgctcatgaagtgaatttgtgtatttggctgaaattcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGCTCTGTGTGCGGTGAAGAGAGTTTTGGAACAG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 11
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
                       ||     | || || | ||  ||        |   | || |    ||  |  |  | |  ||||| || || || |||||||||||||| ||  ||||||||||||| ||||||||  | ||||| ||||||||||| ||||| |
--------------------gtgataggattgctcttgttcttgct--------ttcctacacacgcgtac-atgttgcgttgcagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 11
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
                       ||     |||| || | ||  ||        |   | || |    ||  |  |  | |  ||||| || || || |||||||||||||| ||  ||||||||||||| ||||||||  | ||||| ||||||||||| ||||| |
--------------------gtgataggatttctcttgttcttgct--------ttcctacacacgcgtac-atgttgcgttgcagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG

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|124998568|gb|EL070837.1|EL070837
EST:     CTGCTCTTGATGTCGTTGCAAAAAGCTTGAATTTGAAGTTCTTTGAG                         GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTG
genomic: CTGCTCTTGATGTCGTTGCAAAAAGCTTGAATTTGAAGTTCTTTGAGgtacatgtca ... cacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTG
EST: gi|124977867|gb|EL051142.1|EL051142
EST:     GTCGTTGCAAAAAGCTTGAATTTGAAGTTCTTTGAG                         GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGG
genomic: GTCGTTGCAAAAAGCTTGAATTTGAAGTTCTTTGAGgtacatgtca ... cacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
          taactacataatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA