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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaattagactcattcaaattatcgattcattgactagataatattgaataatgccacattacgttctcaagatgctaccttttccgtttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTTTGGTGGTAACAACCGTGCTCAGGTTTTCTTCAAGCAACATGGATGGACT

Basic information

species Arabidopsis thaliana
transcript AT4G17890.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 2
------ttgaaattagactcattcaaattatcg--attcattgactagataatattgaataatgccacattacgttctcaagatgctaccttttccgtttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTTTGGTGGTAACAACCGTGCTCAGGTTTTCTTCAAGCAACATGGATGGACT
       |||||        ||||| | | | |  | |  |||| |||| |  |  |||  |||    ||  |      |||    ||  |  ||  | | | | ||| || || ||||||||||| ||||| || ||||| || |  |||||||  ||||| || ||||| ||||| ||||||||||| ||||||||||| |||| |
tattctgtgaaacacactatattcagaatgtaggaagttgttgaatagaaagaacagaa--atgattgatagc-----taagtaaatatatgctct-tctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT
















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|116481523|gb|EG524115.1|EG524115
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015086|gb|DR310832.1|DR310832
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015069|gb|DR310815.1|DR310815
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015085|gb|DR310831.1|DR310831
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015088|gb|DR310834.1|DR310834
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015079|gb|DR310825.1|DR310825
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015073|gb|DR310819.1|DR310819
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015078|gb|DR310824.1|DR310824
EST:     GATTGTT---CTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015066|gb|DR310812.1|DR310812
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015063|gb|DR310809.1|DR310809
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCAGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015065|gb|DR310811.1|DR310811
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015081|gb|DR310827.1|DR310827
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGNGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTACACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015089|gb|DR310835.1|DR310835
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015093|gb|DR310839.1|DR310839
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015090|gb|DR310836.1|DR310836
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015077|gb|DR310823.1|DR310823
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015092|gb|DR310838.1|DR310838
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015076|gb|DR310822.1|DR310822
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015067|gb|DR310813.1|DR310813
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015064|gb|DR310810.1|DR310810
EST:     ATTGTTCAGCTACTCACCGGAAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGGACAATGATGT
genomic: ATTGTTCAGCTACTCACCGGAA-TCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGG-ACAATGATGT
EST: gi|86015084|gb|DR310830.1|DR310830
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015094|gb|DR310840.1|DR310840
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015075|gb|DR310821.1|DR310821
EST:     TATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGAC
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGAC
EST: gi|86015071|gb|DR310817.1|DR310817
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015072|gb|DR310818.1|DR310818
EST:     TATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015074|gb|DR310820.1|DR310820
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015080|gb|DR310826.1|DR310826
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015070|gb|DR310816.1|DR310816
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015068|gb|DR310814.1|DR310814
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|19879081|gb|AU239912.1|AU239912
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|86015091|gb|DR310837.1|DR310837
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
EST: gi|152035562|gb|BP858031.2|BP858031
EST:     GATTGTTCAGCTACTCACCGGAATCTTGGTGTT-ATATCAGCTTCGTCAG                         ATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT
genomic: GATTGTTCAGCTACTCACCGGAATCTTGGTGTTCATATCAGCTTCGTCAGgtaaacaatt ... ttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaataatgccacattacgttctcaagatgctaccttttccgtttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTTTGGTGGTAACAACCGTGCTCAGGTTTTCTTCAAGCAACATGGATGGACT
                                ctaccttttccgtttt  CT-rich tract
                                            tttttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaattagactcattcaaattatcgattcattgactagataatattgaataatgccacattacgttctcaagatgctaccttttccgtttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTTTGGTGGTAACAACCGTGCTCAGGTTTTCTTCAAGCAACATGGATGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA