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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagagctgttggcttctgtttgccgcatcaatctctttatttaatacttattagttattgaccagatggtttttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT

Basic information

species Arabidopsis thaliana
transcript AT4G30920.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G028114_T01 (Zea mays), 3'ss of exon 8
----------------------gtactagagctgtt---ggcttctgtttgccgcatcaatctctttatttaatacttattagttattgaccagatggtttttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
                       || | |   | |     | |     | | |   |  ||       |||  || || |   ||||    ||  ||    |   || ||| ||||||||||||||||| |||||||| ||||||   || ||||| |||||||| || |||||||| || || ||| |  |||| || || ||||   | 
gtttgtagtacttgccacatatttagtgggtttatgaaaagttagaagtagacaagtagatggaaccgtttgttatttttc--ttatgcttcaattgccaatgaatc-cagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAACATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTATATTTGGTGCAGCTAAAGATTTG

upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G178958_T01 (Zea mays), 3'ss of exon 4
----------------------gtactagagctgtt---ggcttctgtttgccgcatcaatctctttatttaatacttattagttattgaccagatggtttttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
                       || | |   | |     | |     | | |   |  ||       |||  || || |   |||| |    | | |    ||    ||| ||||||||||||||||| |||||||| ||||||   || ||||| |||||||| || |||||||| || || |||||  |||| || || |||||  | 
gtttgtagtacttgccacatatttagtgggtttatgaaaagttagaagtagacaagtagatggaaccgtttgttatttttc--ttat-gcttggtttgccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG

upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G126913_T01 (Zea mays), 3'ss of exon 4
-------------gtactagagct-gttggcttctgtttgccgcatcaatctctttatttaatacttattagttattgaccagatggtt--tttgttca------cagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
             |    | |  | || || || |    |    |   |      ||  |   ||   || ||||||   |  ||| ||  ||||   |      ||| ||||||||||||||||| |||||||| ||||||   || ||||| |||||||| || |||||||| || || |||||  |||| || || |||||  | 
gtttgtagtacttgccacatatttagtgggtttataaaagttagaagtagacaagtagatggaacc-gtttgttatttttcttatgcttgatttgccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG

upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G018558_T01 (Zea mays), 3'ss of exon 4
-------------gtactagagctgttgg-cttctgtttgccgcatcaatctctttatttaatacttattagttattgaccagatggtt--tttgttca------cagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
             |    | |  | ||||  || |    |    |   |      ||  |   ||   || ||||||   |  ||| ||  ||||   |      ||| ||||||||||||||||| |||||||| |||| |   || ||||| |||||||| || |||||||| ||  | |||||  |||| || || |||||  | 
gtttgtagtacttgccacatatttattgggtttataaaagttagaagtagacaagtagatggaacc-gtttgttatttttcttatgcttgatttgccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTACAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTACAGCTGTATTTGGTGCAGCTAAAGCTTTG

upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G388453_T01 (Zea mays), 3'ss of exon 7
-------------gtactagagct-gttggcttctgtttgccgcatcaatctctttatttaatacttattagttattgaccagatggtt--tttgttca------cagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
             |    | |  | || || || |    |    |   |      ||  |   ||   || ||||||   |  ||| ||  ||||   |      ||| ||||||||||||||||| |||||||| |||| |   || ||||| |||||||| || |||||||| || || |||||  |||| || || |||||  | 
gtttgtagtacttgccacatatttagtgggtttataaaagttagaagtagacaagtagatggaacc-gtttgttatttttcttatgcttgatttgccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTACAGCATCGAGCTAATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG

upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 4
----------gtactagagctgttggc-ttctgtttgccgcatcaatctctttatttaatacttattagttattgacc-agatggttt--ttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
           || |  |  |  |    |  |  |      |   ||  | |   |||||   | | | |||||  |  |  | || |   | ||   || |||||||||||||| || || || |||||||| | |||||||||||||||||| |||||||| |||||||| || ||| | ||  | ||||||||  | 
ttattttttcttattcaatataataaaatattcatcattataatgataacatctattaatctctttgatttattttcttatgttgtctacatattattagTGGTGGCTACAACATCAAGACTGGACCTGGCTGTTCAATTGAGCTCATGAAATTTGATATGGGTGGTTCAGCAGCAGTTTTAGGAACAGCAAAAGCTCTC

upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G08150.1 (Glycine max), 3'ss of exon 4
----------gtactagagctgttgg--cttctgtttgccgcatcaatctctttatttaatacttattagttattgacc-agatggttt--ttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
           || |  |  |  |      ||  |       || ||    | ||||||   ||| | | |||||     |  | || |   | ||   || |||||||||||||| || || || |||||||| | |||||| ||||||||||| |||||||| |||||||| || ||| | ||  | || |||||  ||
taattgattcttatttaatataataaaatatccatcattataatgaaaacgtctatttatctctt-taaattattattttatgttgtctgcatattattagTGGTGGCTACAACATCAAGACTGGACCTGGCTGTTCAATTGAACTCATGAAATTTGATATGGGTGGTTCAGCAGCAGTTTTAGGAACAGCGAAAGCTCTT

upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 4
gtactagagctgttggcttct-----gtttgccgcatcaatctctttatt--taatacttattagttattgaccagatggtttt-------tgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
 | || ||| || ||| | ||         |  |  |  | |     | |  ||||    |||  |  |||  |   |  ||||       ||||   || |||||||||||||| || || || |||||||| || ||||| || |||||||| |||||||| ||||| ||||| ||| |||| || ||||||||  | 
ttgctggaggtgctggttcctcgaaaaccagagggtttgaacctaacagtaataattacaatttttctttgttcttttttttttatttgcatgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAAATTTGATATGGGCGGTTCTGCTGCAGTTTTTGGAGCAGCAAAAGCTCTA

upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 4
----------gtactagagctgttgg--cttctgtttgccgcatcaatctctttatttaatacttattagttattgacc-agatggttt--ttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
           || |  |  |  |      ||  |       || ||    | ||||||   ||| | | |||||     |  | || |   | ||   || |||||||||||||| || || || |||||||| | |||||| ||| ||||||| |||||||| |||||| |  | ||| | ||  |  | |||||  ||
taattgattcttatttaatataataaaatatccatcattataatgaaaacgtctatttatctctt-taaattattattttatgttgtctgcatattattagTGGTGGCTACAACATCAAGACTGGACCTGGCTGTTCAATTGAACTCGTGAAATTTGATATGGGTGGTTCAACAACAGTTTTAGGAACAACGAAAGCTCTT

upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 4
-----gtactagagctgttggcttctgtttgccgcatcaatctctttatttaatact-------tattagttattgaccagatggtttttgt--tcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
      | | | |  ||     |    |   |    | | | | |  |||| || ||       ||   ||| || | ||  |   |||  |  |   || |||||||||||||| || || || |||||||| |  |||||||||||||| || |||||||| ||||||||||| ||||| || || ||||||||||||
tttgttttcaaaaagtggccagtataataatctatgttattatgtgcatttgattctccatctatacgtgttcttaaacatttatctttcatggttttagTGGTGGCTACAACATCAAGACTGGACCTGGCTGTTCTATTGAGCTCATGAAGTTTGATATGGGGGGTTCAGCTGCGGTTCTCGGTGCAGCAAAAGCCATT

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|125139005|gb|EL177996.1|EL177996
EST:     CCTGTTAAAACAAAACTTGCTCTTGTTGGAAAAGGATTGACATTTGACAG                         CGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATAGA
genomic: CCTGTTAAAACAAAACTTGCTCTTGTTGGAAAAGGATTGACATTTGACAGgtactagagc ... ttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCAT-GA
EST: gi|125239811|gb|EL253896.1|EL253896
EST:     CTGTTAAAACAAAAACTTGCTCTTGTTGGAAAAGGATTGACATTTGACAG                         CGGTGGCTACAACATTAAAACCGGGCCTGG
genomic: CTGTTAAAAC-AAAACTTGCTCTTGTTGGAAAAGGATTGACATTTGACAGgtactagagc ... ttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatctctttatttaatacttattagttattgaccagatggtttttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT
                            tattgac  putative branch site (score: 2)
                                          tttttgttc  putative PPT
      tctttatttaatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactagagctgttggcttctgtttgccgcatcaatctctttatttaatacttattagttattgaccagatggtttttgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT