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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaagtttgttttcgtatcttgtttggaggttttggaattgtggtttttggtgttaacttttttatcggatgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGAGCTTCCTGGTCCTTGTTTACTG

Basic information

species Arabidopsis thaliana
transcript AT2G05590.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G05590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G21320.1 (Glycine max), 3'ss of exon 3
-----------gtaaggaagtttgttttcgtatcttgtttggaggttttggaattgtggtttttggtgttaacttt--tttatcggatgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGAGCTTCCTGGTCCTTGTTTACTG
            |   |   ||  | |  | ||     |     || |||  ||  ||   | | |  | ||| ||  ||  ||| |||||||||||||||||||||||||| ||||| |||||||| ||| | || |  ||||   | ||| |||||||| |||| |||
gtaattttgctttctagtttttaatctgtgcattgaactgtattgtgttgttatgttgaaatattgattcaacattacttcttcgaatgaagggcagTACGTTGAAACATGGCATATCGCTTCGTACACTTCTTCGCAACAGTGATAAACTTTCTGGTCCTGGTTTGCTG

upper sequence: AT2G05590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G34240.1 (Glycine max), 3'ss of exon 2
---------gtaaggaagtttgttttcgtatcttgtttggaggttttggaattgtggt----ttttggtgtta-acttttttatcggatgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGAGCTTCCTGGTCCTTGTTTACTG
          |  | | ||||   ||  |   |||    |   |||||  ||||   |    | ||| |   | | || ||  |   || |||||||||||||| ||||||||  ||||||||||||| ||| | || |  ||||  |||||| || ||||| |||| |||
gtaactttcctctgtaggttttgatttatgcattgaacagta-ttttgctattgctttgaaatattgattcaacatttgttctttaaattaagggcagTACGTTAAAACATGGAGTATCACTTCGTACACTTATTCGCAAGAGTGCTGAGCTTTCTTGTCCTGGTTTGCTG

upper sequence: AT2G05590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g01850.t01 (Vitis vinifera), 3'ss of exon 2
gtaaggaagtttgttttcg------tatcttgtttggag-gttttggaattgtggtttttggtgttaacttt---tttatcggatgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGAGCTTCCTGGTCCTTGTTTACTG
     ||  |||| |  |       || | ||  |     | | | | ||| ||||||||| | | | || |     | |   ||||||||||||||||||||||||||||||||||| || || ||| | || |  ||||  || ||| ||||||||||||| |||
---gtgagttttgctaacaaagtaatagcctgcataagttgctcttgtatt-tggtttttgat-tcagctctgatcgtttaaaatgaagggcagTACGTTGAAACATGGTATATCACTCCGCACACTTATTCGTAAGAGTGCTGACCTTTCTGGTCCTTGTTTGCTG

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|116400808|gb|EG443400.1|EG443400
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400387|gb|EG442979.1|EG442979
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400804|gb|EG443396.1|EG443396
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|116400804|gb|EG443396.1|EG443396
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|116400804|gb|EG443396.1|EG443396
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|116400804|gb|EG443396.1|EG443396
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|116400804|gb|EG443396.1|EG443396
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|116400804|gb|EG443396.1|EG443396
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|116400393|gb|EG442985.1|EG442985
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116398153|gb|EG440745.1|EG440745
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400818|gb|EG443410.1|EG443410
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCCTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400408|gb|EG443000.1|EG443000
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400813|gb|EG443405.1|EG443405
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCCTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400389|gb|EG442981.1|EG442981
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400416|gb|EG443008.1|EG443008
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400815|gb|EG443407.1|EG443407
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116398152|gb|EG440744.1|EG440744
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTTATATCACTTCGTACGCTTTTGCGAAAGAAGTGGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGT-ATATCACTTCGTACGCTTTTGCGAA-GAAGTGGA
EST: gi|116400414|gb|EG443006.1|EG443006
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116398150|gb|EG440742.1|EG440742
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400807|gb|EG443399.1|EG443399
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|86072717|gb|DR368474.1|DR368474
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86072717|gb|DR368474.1|DR368474
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86072717|gb|DR368474.1|DR368474
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86072717|gb|DR368474.1|DR368474
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86072717|gb|DR368474.1|DR368474
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86072717|gb|DR368474.1|DR368474
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|116400810|gb|EG443402.1|EG443402
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCCTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400410|gb|EG443002.1|EG443002
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|86069621|gb|DR365378.1|DR365378
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86069621|gb|DR365378.1|DR365378
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86069621|gb|DR365378.1|DR365378
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86069621|gb|DR365378.1|DR365378
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86069621|gb|DR365378.1|DR365378
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|86069621|gb|DR365378.1|DR365378
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         G
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcag-
EST: gi|116400814|gb|EG443406.1|EG443406
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGA
EST: gi|116400412|gb|EG443004.1|EG443004
EST:     GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAG                         TACGTTGAAACATGGTTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAG
genomic: GCGAGTCTTCCTAATATTGTAAGAGGATGCAAATGGATCTTGTTGTATAGgtaaggaagt ... tgaagggcagTACGTTGAAACATGGT-ATATCACTTCGTACGCTTTTGCGAAGAAGTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaggttttggaattgtggtttttggtgttaacttttttatcggatgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGAGCTTCCTGGTCCTTGTTTACTG
                          tgttaac  putative branch site (score: 2)
                          tgttaacttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaagtttgttttcgtatcttgtttggaggttttggaattgtggtttttggtgttaacttttttatcggatgaagggcagTACGTTGAAACATGGTATATCACTTCGTACGCTTTTGCGAAGAAGTGGAGAGCTTCCTGGTCCTTGTTTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT