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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttgctttttatcatctcaaatcaatggaacatcaatcggttctgttctcattgatttctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAACCGGTAAGAAGTTTTGCATTTGCGTGAAAGAAGTTCTTCCATGGGTGATG

Basic information

species Arabidopsis thaliana
transcript AT2G17695.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G17695.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G22910.1 (Glycine max), 3'ss of exon 3
------gtatgttttgctttttatcatctcaaatcaatggaac---atcaatcggt-----tctgttctcattgattt------------ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAACCGGTAAGAAGTTTTGCATTTGCGTGAAAGAAGTTCTTCCATGGGTGATG
       || | |||  || || |  |   | |  | |         | ||  |||     | ||||  ||| |||||             |  |||||||||||||||  || |||||||||||||||||||    ||||| ||  ||   ||   |||||| ||  |||| || || ||  |  | || ||| | |||
agtgggataagattttgttgttgttgttgtagagaagtttgcttcttttaaggggtgtgtgtgtgtttacatagatttaatgtgggaaaattccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACAAGGAGTGAAGTTCTGTGTTTGTGTCAAGGAGTTCTTCCCGTGGCTCATG
















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|86061786|gb|DR357543.1|DR357543
EST:     TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAA                         GCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
genomic: TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAAgtatgttttg ... ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
EST: gi|86086361|gb|DR382120.1|DR382120
EST:     TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAA                         GCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
genomic: TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAAgtatgttttg ... ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
EST: gi|86077284|gb|DR373041.1|DR373041
EST:     TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAA                         GCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
genomic: TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAAgtatgttttg ... ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
EST: gi|19878362|gb|AU239193.1|AU239193
EST:     TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAA                         GCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
genomic: TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAAgtatgttttg ... ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
EST: gi|86061618|gb|DR357375.1|DR357375
EST:     TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAA                         GCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
genomic: TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAAgtatgttttg ... ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
EST: gi|86061787|gb|DR357544.1|DR357544
EST:     TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAA                         GCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTG
genomic: TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAAgtatgttttg ... ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTG
EST: gi|86084935|gb|DR380694.1|DR380694
EST:     TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAA                         GCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
genomic: TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAAgtatgttttg ... ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAAC
EST: gi|86061788|gb|DR357545.1|DR357545
EST:     TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAA                         GCATTTTGGTATGGATTGGGCATTTGTTGA
genomic: TCTGGTAGAGAGAGTTATGAGAAGGGCAAAAAAGCTCTCCAGAATTGGAAgtatgttttg ... ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcaaatcaatggaacatcaatcggttctgttctcattgatttctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAACCGGTAAGAAGTTTTGCATTTGCGTGAAAGAAGTTCTTCCATGGGTGATG
                                           ttctaat  putative branch site (score: 2)
                                          tttct  CT-rich tract
                                     attgatttctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttttgctttttatcatctcaaatcaatggaacatcaatcggttctgttctcattgatttctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAACCGGTAAGAAGTTTTGCATTTGCGTGAAAGAAGTTCTTCCATGGGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT