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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaatctcctcttaacacttccttatagtctctctgtataggacttgactgactcttatgctcggttgtttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCTTCCAGAGATATTTGCATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCT

Basic information

species Arabidopsis thaliana
transcript AT5G16150.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G07780.2 (Glycine max), 3'ss of exon 12
----------------------------------------gtaagtcaatctcctcttaac--acttccttatagtctctctgtataggacttga----ctgac--tcttatgctcggttg-tttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCTTCCAGAGATATTTGCATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCT
                                        || |   | |      | ||   ||||   | |  | |   | | || |||||      ||||      |||| ||  |   ||| || ||| |||||||| || ||||| ||||||||||| || || || || |||||||| || ||||||||||| ||  |||| ||||||||||| ||  || | || 
gtaagtcatttaattttgtcaataatagtgattccattcagtgaacgacttaaacttcaatgaacttatatgttcttttattatttaagacttacatttctgatgactctatgttctatgaattttaaccagCTATGTCCTATCCTTCTCTCTTGGTGCTGGTCCTGTGCCTGCCCTTCTTCTACCGGAGATATTTGCTTCTAGAATTAGAGCAAAAGCAGTTTCTTTGTCA

upper sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------------gtaagtcaatctcctcttaacacttccttatagtctctctgtataggacttgactgact----cttatgctcggttgtttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCTTCCAGAGATATTTGCATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCT
                              |  |||  |   ||||    |     || |  | | ||   ||   ||       |||    |||    ||  |   || |  ||| |||||  |||| ||||| ||||||||||| || || || ||||||||||||||||| |||||||| ||  ||||||| |||||||| || ||| | || 
gtaagttgatacttttccttatcatattgatgtgtcttttctctctaccaatccatttcttctttttcccaatctaacccaggatacttgaacttgctatctttccatttatgcagCTATGTGTTGTCCTTCTCTCTTGGTGCTGGTCCTGTCCCTGCTCTTCTTCTTCCAGAAATATTTGCCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCA
















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|116412120|gb|EG454712.1|EG454712
EST:     AAGGCTCTTGCTGCCTATTCTGGAACCCTTGCCGTTGTTGGAACTGTTCT                         ATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCT
genomic: AAGGCTCTTGCTGCCTATTCTGGAACCCTTGCCGTTGTTGGAACTGTTCTgtaagtcaat ... tttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCT
EST: gi|125016210|gb|EL088479.1|EL088479
EST:     AAGGCTCTTGCTGCCTATTCTGGAACCCTTGCCGTTGTTGGAACTGTTCT                         ATATGTCCTGTCATTCTCACTTGGTGCTGGCC
genomic: AAGGCTCTTGCTGCCTATTCTGGAACCCTTGCCGTTGTTGGAACTGTTCTgtaagtcaat ... tttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCC
EST: gi|124968299|gb|EL042264.1|EL042264
EST:     TCTTGCTGCCTATTCTGGAACCCTTGCCGTTGTTGGAACTGTTCT                         ATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCT
genomic: TCTTGCTGCCTATTCTGGAACCCTTGCCGTTGTTGGAACTGTTCTgtaagtcaat ... tttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCT
EST: gi|124735206|gb|EH826608.1|EH826608
EST:     AAGGCTCTTGCTGCCTATTCTGGAACCCTTGCCGTTGTTGGAACTGTTCT                         ATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTC
genomic: AAGGCTCTTGCTGCCTATTCTGGAACCCTTGCCGTTGTTGGAACTGTTCTgtaagtcaat ... tttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTC
EST: gi|125289329|gb|EL303414.1|EL303414
EST:     ACCCTTGCCGTTGTTGGAACTGTTCT                         ATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCT
genomic: ACCCTTGCCGTTGTTGGAACTGTTCTgtaagtcaat ... tttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCT
EST: gi|86081281|gb|DR377038.1|DR377038
EST:     TGCCGTTGTTGGAACTGTTCT                         ATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCT
genomic: TGCCGTTGTTGGAACTGTTCTgtaagtcaat ... tttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtctctctgtataggacttgactgactcttatgctcggttgtttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCTTCCAGAGATATTTGCATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCT
                       gactgac  putative branch site (score: 2)
                                          ttgtttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaatctcctcttaacacttccttatagtctctctgtataggacttgactgactcttatgctcggttgtttaaatcagATATGTCCTGTCATTCTCACTTGGTGCTGGCCCGGTACCGGCTCTTCTTCTTCCAGAGATATTTGCATCCCGAATCAGAGCAAAAGCCGTCGCTCTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA