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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttgtttctgttagtcttgtattttgcacctttaaaagaagagagagaggtaaaaagaatcaactatctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATTGACAGCTACTAAATGAGCTTTTGTTTGCTCTAAAACAAAACTGCTCTTT

Basic information

species Arabidopsis thaliana
transcript AT5G04740.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G04740.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G42580.4 (Glycine max), 3'ss of exon 8
----------------------------------------------------------------------------------------------------gtaagtttttgtttctgttagtcttgtattttgcacctttaaaagaagagagagaggtaaaaagaatcaactatctcct-------gcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATTGACAGCTACTAAATGAGCTTTTGTT-TGCTCTAAAACAAAACTGCTCTTT
                                                                                                     |||||   | || || ||| ||    |    |    | |     |    |  |    |  ||   |    | |    |       ||||||||||||||| ||||||||||||| |||| ||| ||| || || || |||||||| |||| ||  | |     || ||   |||  ||| ||     || 
gtaacctttgtgttcaaagaaatggagaaatttttcctagatgctggagtagaagtaatttagcaatcgtttgtttatctaactattgcattgattttaaataagtcggttttcctttta-tccaacaccaagtcattctgctgaatttaattgcacaacgaactcttttttgtggttttgaatgagcagGTTTTGGTGAATTGTCTGCGTTACTACCTGCGAACGCCAGAGACAGATATTGACAGTTACTGAAGAAACCACCCTTGTGAAATAAGCCAATACAATGGTT-

upper sequence: AT5G04740.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G24450.3 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------------------------------------------------gtaagtttttgtttctgttagtcttgtattttgcacctttaaaagaagagagagaggtaaaaagaatcaactatct----cctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATTGACAGCTACTAAATGAGCTTTTGTT-TGCTCTAAAACAAAACTGCTCTTT
                                                                                                            ||  ||||   |||     |        |  | ||  ||    |    |     | |   ||  | |     || |       ||||||||||||||| ||||||||||||| |||| | | ||| || || || ||||| || |||| || || |     || |    |||  |||  |     || 
gtaaccctcgtgttcaaagaaatggagaaatttttccaatatgctgaggaagaactaatttaggaatcgtttgtttatctgactaactattgcattgattttaaataagtcggtttgccttttatccaacaccaagtcattcattttgctgaatttaattgcacggggaattattttgtgattttgaatgagcagGTTTTGGTGAATTGTCTGCGTTACTACCTGCGGACGCCAGAGACAGATATTGATAGTTACTGAAGGAACCACCCTTGTAAAATAAGCCAATGCAATGGTT-
















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|86079610|gb|DR375367.1|DR375367
EST:     AGTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAG                         GTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT
genomic: AGTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAGgtaagttttt ... tctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT
EST: gi|125277659|gb|EL291744.1|EL291744
EST:     AGTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAG                         GTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGG
genomic: AGTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAGgtaagttttt ... tctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGG
EST: gi|125207495|gb|EL222449.1|EL222449
EST:     CTCTAAACAGATCTTTGTCACAG                         GTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT
genomic: CTCTAAACAGATCTTTGTCACAGgtaagttttt ... tctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT
EST: gi|124867621|gb|EH952058.1|EH952058
EST:     GTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAG                         GTTTTGGTGAACTGTCTGCGTTACTTCCTG
genomic: GTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAGgtaagttttt ... tctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTG
EST: gi|125148772|gb|EL182269.1|EL182269
EST:     AGATCTTTGTCACAG                         GTTTTGGTTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACAT
genomic: AGATCTTTGTCACAGgtaagttttt ... tctcctgcagGTTTTGG-TGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACAT
EST: gi|125043750|gb|EL116019.1|EL116019
EST:     GATCTTTGTCACAG                         GTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT
genomic: GATCTTTGTCACAGgtaagttttt ... tctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT
EST: gi|116403963|gb|EG446555.1|EG446555
EST:     AGTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAG                         GTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT
genomic: AGTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAGgtaagttttt ... tctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT
EST: gi|124955062|gb|EL030104.1|EL030104
EST:     GTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAG                         GTTTTGGTGAACTGTCTGCGTTACTT
genomic: GTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAGgtaagttttt ... tctcctgcagGTTTTGGTGAACTGTCTGCGTTACTT
EST: gi|86082088|gb|DR377847.1|DR377847
EST:     AGTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAG                         GTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT
genomic: AGTTTCACGTAAGCTACCAAGGGCAAGCTCTAAACAGATCTTTGTCACAGgtaagttttt ... tctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcacctttaaaagaagagagagaggtaaaaagaatcaactatctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATTGACAGCTACTAAATGAGCTTTTGTTTGCTCTAAAACAAAACTGCTCTTT
                                          ctatctcct  CT-rich tract
         tttaaaagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttgtttctgttagtcttgtattttgcacctttaaaagaagagagagaggtaaaaagaatcaactatctcctgcagGTTTTGGTGAACTGTCTGCGTTACTTCCTGAGAAGGCCTGAAACTGACATTGACAGCTACTAAATGAGCTTTTGTTTGCTCTAAAACAAAACTGCTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT