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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctttcagcttacaacttatcagtttttaaggggtcaaatcgaattatctgtgcctctctctttctctacaagtatctaacaataatagttttgtttttttaaagGTATGGACAACAGGAACTATGGGAGAACTAAGCCCG

Basic information

species Arabidopsis thaliana
transcript AT3G05190.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 18
gttctttcagcttacaacttatcagtttttaaggggtcaaatcgaattatctgtgcctctctctttctctacaagtatctaacaataatagttttgtttttttaaagGTATGGACAACAGGAACTATGGGAGAACTAAGCCCG
     |  |  ||    | | ||| |||||           ||  |   | | |  ||||     | | ||     ||| |   ||||       | |   ||  || |||||||||||||||| ||||||||||||||||| 
-----tataagttttggcct-tca-tttttctctttctgcctcccaccctttctctctcttcaaatttatatcgagatcgagttataactagaaggctgcgttgcagATATGGACAACAGGAACAATGGGAGAACTAAGCCCA

upper sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 17
gttctttcagcttacaacttat-cagtttttaaggggtcaaatcgaattatctgtgcctctctctttctctacaagtatctaacaataatagttttgtttttttaaagGTATGGACAACAGGAACTATGGGAGAACTAAGCCCG
     | ||   |     |  |  | ||| |    |    | |  |  | || ||   | | |  | |  |  | ||   ||  | ||  ||  |||| ||    ||||||||||| || ||||| ||||||||||||||||||
-----tccatagtcgggttggtgtaatttatggcagtgttagtttatctctccgtatatatttggtccaatttatgttgttataactagaagacttgtctt---gaagGTATGGACGACTGGAACAATGGGAGAACTAAGCCCG

upper sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA03G40000.1 (Glycine max), 3'ss of exon 17
gttctttcagcttacaacttat-cagtttttaaggggtcaaatcgaattatctgtgcctctctctttctctacaagtatctaacaataatagttttgtttttttaaagGTATGGACAACAGGAACTATGGGAGAACTAAGCCCG
     | ||   |     |  |  | ||| |    |    | | ||  | ||  |   | | |  | |  |  | ||   ||  | ||  ||   ||| ||    ||||||||||| || ||||| ||||||||||||||||| 
-----tccatagtcgggttggtgtaatttatggcagtgttagttgatctctccttatatatttggtccaatttatgttgttataactagaagacctgtctt---gaagGTATGGACGACTGGAACAATGGGAGAACTAAGCCCC

upper sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 27
gttctttcagcttacaacttatcagtttttaaggggtcaaatcgaattatctgtgcctctctctttctctacaagtatctaacaataatagttttgtttttttaaagGTATGGACAACAGGAACTATGGGAGAACTAAGCCCG
  |||   | ||| | |   |   |    |    | ||||||| | ||   | |     | |  | || |   |||    ||||  || | |  |  ||  ||  ||||||||||||| ||||| ||||||||||| ||||| 
-atctagtaacttgctataaaagtgcccattctagctcaaatctattttcttttaaacattttatgcttttagagt----aacagcaaaaatgct--ttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA

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|163975450|gb|ES025174.1|ES025174
EST:     TCTTAGAAGAAAGAAGAATCAGTCTCTCCGAATTCCATACAGCTAATGAG                         GTATGGACAACAGGAACTATGGGAGAACTAAGCCCG
genomic: TCTTAGAAGAAAGAAGAATCAGTCTCTCCGAATTCCATACAGCTAATGAGgttctttcag ... ttttttaaagGTATGGACAACAGGAACTATGGGAGAACTAAGCCCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcctctctctttctctacaagtatctaacaataatagttttgtttttttaaagGTATGGACAACAGGAACTATGGGAGAACTAAGCCCG
                        atctaac  putative branch site (score: 2)
                                       ttttgttttttt  putative PPT
                    aagtatctaacaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctttcagcttacaacttatcagtttttaaggggtcaaatcgaattatctgtgcctctctctttctctacaagtatctaacaataatagttttgtttttttaaagGTATGGACAACAGGAACTATGGGAGAACTAAGCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA