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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatattcacatcattccaacactcttaaacccgagaattatgattgtatcttcaaagatagatgattaatcaatatctctcttgtgtttgcaatgcagGCGTTTGGATGGGCATACATGTACAGCTCCCACAACACATGGGACCATATCTACGTCTACTGGATCAGTTCTTTCGTAGGAGCATTATCTGCTGCATTGC

Basic information

species Arabidopsis thaliana
transcript AT3G04090.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G04800.1 (Glycine max), 3'ss of exon 2
---catatattcacatcattccaacactcttaaacccgagaattatgattgtatcttcaaagatagatgattaatcaatatctctcttgtgtttg-caatgcagGCGTTTGGATGGGCATACATGTACAGCTCCCACAACACATGGGACCATATCTACGTCTACTGGATCAGTTCTTTCGTAGGAGCATTATCTGCTGCATTGC
   ||| | ||   ||| |||  |   |  ||       || ||| | |  ||   | | ||||     || ||| | | | |    |||  ||| |  ||||||| ||||| |||||||||||  ||| ||  |||||||||||||||||  |||| || ||||||||  |  | ||||  |||||| |||  ||||| | ||
tctcatgtttttgaatc-ttctgatgttaatatcagtttga-ttagggtc-tagacttagagattc-caatgaataactttgtgatgtgttattgtccctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCGCCGGAGCAATATTGGCTGCTTGGC
















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|116485953|gb|EG528545.1|EG528545
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGG
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGG
EST: gi|116485960|gb|EG528552.1|EG528552
EST:     TTGTTGTCGCCTGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGG
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGG
EST: gi|116485956|gb|EG528548.1|EG528548
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGG
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGG
EST: gi|116485961|gb|EG528553.1|EG528553
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGG
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGG
EST: gi|116485957|gb|EG528549.1|EG528549
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGG
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGG
EST: gi|116485972|gb|EG528564.1|EG528564
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGG
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGG
EST: gi|116485968|gb|EG528560.1|EG528560
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGG
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGG
EST: gi|116485976|gb|EG528568.1|EG528568
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGG
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGG
EST: gi|125194667|gb|EL209621.1|EL209621
EST:     CACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGGCATACATGTACAGCTCCCACAACACATGGGACCATATC
genomic: CACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGGCATACATGTACAGCTCCCACAACACATGGGACCATATC
EST: gi|125040526|gb|EL112795.1|EL112795
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGGCATACATGTACAGCT
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGGCATACATGTACAGCT
EST: gi|116485955|gb|EG528547.1|EG528547
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGG
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGG
EST: gi|86087625|gb|DR383384.1|DR383384
EST:     TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATT                         GCGTTTGGATGGGCATACATGTACAGCTCCCACAACACATGGGACCATATC
genomic: TTGTTGTCGCCGGATCTAAATACACTGGACCAGCCATGAATCCTGCCATTgtaagtatac ... tgcaatgcagGCGTTTGGATGGGCATACATGTACAGCTCCCACAACACATGGGACCATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatcttcaaagatagatgattaatcaatatctctcttgtgtttgcaatgcagGCGTTTGGATGGGCATACATGTACAGCTCCCACAACACATGGGACCATATCTACGTCTACTGGATCAGTTCTTTCGTAGGAGCATTATCTGCTGCATTGC
                    gattaat  putative branch site (score: 3)
                                tctctcttgtgttt  putative PPT
                  atgattaatcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatattcacatcattccaacactcttaaacccgagaattatgattgtatcttcaaagatagatgattaatcaatatctctcttgtgtttgcaatgcagGCGTTTGGATGGGCATACATGTACAGCTCCCACAACACATGGGACCATATCTACGTCTACTGGATCAGTTCTTTCGTAGGAGCATTATCTGCTGCATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - -attcaca
- - - - - - - - -ccaacac
- - - - - - - - - - - - - ttaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - -cttcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taatcaa