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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTGAAATCGGAGATCTAATCACACAGCTCGAGTCTAAGAACCCTACTCCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagtttttttccggtgaaaactttctcttgtagtcctgtagatagcatcattcgtaggattctggattcaaatggtagatctcgtgctgcttttgatttggttaaacctcttttgcag

Basic information

species Arabidopsis thaliana
transcript AT4G22240.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22240.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ38264 (Selaginella moellendorffii), 5'ss of exon 1
GAGCTGAAATCGGAGATCTAATCACACAGCTCGAGTCTAAGAACCCTACTCCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagtttttttccggtgaaaactttctcttgtagtcctgtagatagcatcattcgtaggattctggattcaaatggtagatctcgtgctgcttttgatttggttaaacctcttttgcag
|||| ||  |    || || ||||| ||||| ||  ||||||| || |||||||||||||| |||||  |   | | ||||| |||||||||||||||||||||||  ||||      |   ||| |||||    | || |   |  | |   || |  |  ||| | | | | |   |||| |    ||| || |                        
GAGCCGAGGTGAATGAGCTCATCACTCAGCTAGAAGCTAAGAATCCAACTCCAGCTCCGACCGAAGCATTGGCCGTGCTCAATGGCAAATGGATCCTCGCgtaagtcctttt------agttcttcctctt----ttctctctctctctttgctctt--gcctcttggt-cgacta--agattttcatctgattctag----------------------

upper sequence: AT4G22240.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ14959 (Selaginella moellendorffii), 5'ss of exon 1
GAGCTGAAATCGGAGATCTAATCACACAGCTCGAGTCTAAGAACCCTACTCCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagtttttttccggtgaaaactttctcttgtagtcctgtagatagcatcattcgtaggattctggattcaaatggtagatctcgtgctgcttttgatttggttaaacctcttttgcag
|||| ||  |    || || ||||| ||||| ||  ||||||| || |||||||||||||| |||||  |   | | ||||| |||||||||||||||||||||||  |||       |   ||| ||||| |    || |   |    |   |  | ||    | || | | ||  |  ||||| | ||                              
GAGCCGAGGTGAATGAGCTCATCACTCAGCTAGAAGCTAAGAATCCAACTCCAGCTCCGACCGAAGCATTGGCCGTGCTCAATGGCAAATGGATCCTCGCgtaagtcctttc------agttcttcctcttttctctctctctttgctcttgcttcttgg----tcgactaagat--ttcatctcattctag----------------------------
















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|301502185|gb|HO207725.1|HO207725
EST:     AATGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
genomic: AATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
EST: gi|47830620|gb|CK120304.1|CK120304
EST:     CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
genomic: CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
EST: gi|47829540|gb|CK119224.1|CK119224
EST:     CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTTTCACGAGGAATCGTACC
genomic: CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
EST: gi|124981963|gb|EL054800.1|EL054800
EST:     CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGC                         CTACACATCGTTCGTG
genomic: CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTG
EST: gi|124891807|gb|EH970709.1|EH970709
EST:     TGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
genomic: TGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
EST: gi|47829696|gb|CK119380.1|CK119380
EST:     CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
genomic: CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
EST: gi|47828628|gb|CK118312.1|CK118312
EST:     CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTTTCACGAGGAATCGTACC
genomic: CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
EST: gi|125201233|gb|EL216187.1|EL216187
EST:     CAAATGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
genomic: CAAATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
EST: gi|124904443|gb|EH978523.1|EH978523
EST:     CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
genomic: CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
EST: gi|301502606|gb|HO208146.1|HO208146
EST:     CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
genomic: CCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTACC
EST: gi|124715282|gb|EH806684.1|EH806684
EST:     CTTTTCCTTCTCAACGGCAAATGGATCCTCGC                         CTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTAAC
genomic: CTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagttttt ... tcttttgcagCTACACATCGTTCGTGAATTTGTTCCCGTTGCTATCACGAGGAATCGTA-C

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTGAAATCGGAGATCTAATCACACAGCTCGAGTCTAAGAACCCTACTCCAGCTCCGACGGAAGCTCTTTTCCTTCTCAACGGCAAATGGATCCTCGCgtaagtttttttccggtgaaaactttctcttgtagtcctgtagatagcatcattcgtaggattctggattcaaatggtagatctcgtgctgcttttgatttggttaaacctcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC