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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacattgattcatacaacgttctattatagtgtgattatttctttctgatctacctaaatttggcacatcaacgaaatttgtcaacttttcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGTCTGTAGGGTTTCTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTT

Basic information

species Arabidopsis thaliana
transcript AT4G22360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22360.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G332809_T01 (Zea mays), 3'ss of exon 7
gcacattgattcatacaacgttcta--ttat-agtgt-gattatttctttctgatctacctaaatttggcacatcaacgaaatttgtcaacttttcctttg---cagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGTCTGTAGGGTTTCTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTT
  |||| |||   | | | ||||||  || | || || |  | |   || ||| | | |   |   ||     | |||  | | |      | |  |  ||   |||||||   | |||| | ||| |||| ||||||||||||||  |||||||||||||| | || |||||||| ||  |||   | ||||||||||| ||    
-gacatggatatgtcccatgttctaagttgtcagcgttggctgtcatttgctggtgttc---agcctgttcactgaactcagtgttcttgttgtggcaatgtagCAGTGCTAGTGTTGGAGCAAAACGAAAAGGTGGTCCTGGAGGGTTAAACAAAGTCTGTGGTGTGTCTCCAGAGCTGCAAGCTATCGTTGGTGAACCAGCC---

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0090g01460.t01 (Vitis vinifera), 3'ss of exon 1
-gcacattgattcat-acaacgttctattatagtgtgattatttctttctgatctacctaaatttggcacatcaacgaaatttgtcaacttttcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGTCTGTAGGGTTTCTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTT
 |    |  ||   | ||||| || | |||| |||| ||||| |   | |    | |  |   |||||  |        || |      ||||  | ||||||||||  ||||||||||||||||  |||||||| || || ||||||||||| ||  | ||||| || |||||| |     |||||||  | || || || 
agagtgtgtatctgtcacaacctttt-ttat-gtgttattatatgcctattgcattctgatgcttggcctaatgtttccatgttcatgatttttttctgcagTGCTCGAGCTGGAACTAAAAGAAGAGGTGGTCCAGGGGGTCTAAACAAAGTTTGCGGTGTTTCACCTGAACTTCAGACCATTGTTGGCCAGCCAGCGCTG
















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|47830511|gb|CK120195.1|CK120195
EST:     TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAG                         TGCTCCGGCTGGAACTAAAAGAAAGGGTGGGCCTGGAGGACTAAACAAAGT
genomic: TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAGgtagggtttg ... tcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGT
EST: gi|163999586|gb|EL998698.1|EL998698
EST:     TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAG                         TGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCC
genomic: TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAGgtagggtttg ... tcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCC
EST: gi|47828877|gb|CK118561.1|CK118561
EST:     TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAG                         TGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGT
genomic: TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAGgtagggtttg ... tcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGT
EST: gi|86074539|gb|DR370296.1|DR370296
EST:     TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAG                         TGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGT
genomic: TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAGgtagggtttg ... tcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGT
EST: gi|47830960|gb|CK120644.1|CK120644
EST:     TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAG                         TGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGT
genomic: TCACATGGCGGGAATGCTTCTCTATCTGTTAATCAAGCCCCAAAAGAAAGgtagggtttg ... tcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatctacctaaatttggcacatcaacgaaatttgtcaacttttcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGTCTGTAGGGTTTCTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTT
        acctaaa  putative branch site (score: 3)
                                     tcaacttttccttt  putative PPT
           taaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacattgattcatacaacgttctattatagtgtgattatttctttctgatctacctaaatttggcacatcaacgaaatttgtcaacttttcctttgcagTGCTCCGGCTGGAACTAAAAGAAAGGGTGGTCCTGGAGGACTAAACAAAGTCTGTAGGGTTTCTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - -catacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -acctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacgaaa