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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG

Basic information

species Arabidopsis thaliana
transcript AT5G28840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 2
-------------gttagttagattttgttttcttcggttt--tcgcagtttacggtttcttaaaacaagttaaaaagat--tggattttttgtttgcttt----agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                |   |  | || || | |    ||   | |||   ||  || | |        || | |  |||  | | ||||| ||||  |||    ||||| |||||||| || ||||||||||||||||| || || |||||||||||||| |   ||||||| ||||||||||| ||||| |||||||| |||
gtcattcattttgaacaaacatgtgttattatgtcactttcaattgcatgatatagtctttatgtcgccgtcatagtgatccttgttttttggtttattttttttagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAGCAGTTGGAGACAA---ATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 1
----------------gttagttagattttgttttcttcggtt-----ttcgcagttta-cggtttcttaaaacaagttaaaaaga---ttggattttttgt------ttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                 | | ||  ||| | | || || |        ||     |     || |  ||  |  |  | |  | |    ||     || ||       ||  |  ||||| |||||||| || |||||||||||||| || || ||||| |||||||| ||||   ||||||||||||||||||| ||||| ||||| || |||
gttagccatcatgcacatcatttcaattatttgtttttggaccaaacatttatgatgcggtggctgttttgattagatgatgatgtgttttatgcgttctgaaaaatatttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTTAAACAGTTGGAAACTA---ATGTGAGCTTGAAGGAGTCCGATGCATGGCCAGCTGAG

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 2
-------------gttagttagattttgttttcttcggttt--tcgcagtttacggtttcttaaaacaagttaaaaagat--tggattttttgtttgcttt-----agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                |   |  | || || | |    ||   | |||   ||  || | |        || | |  |||  | | ||||| ||||  |||     ||||| |||||||| || ||||||||||||||||| || || || ||||||||||| |   ||||||| ||||||||||| ||||| |||||||| |||
gtcattcattttaaacaaacatgtgttattatgtcactttcaattgcataatatagtctttatgtcgctgtcatagtgatccttgttttttggtttattttttttaagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCTGAATTCAAACAGTTGGAGACAA---ATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G43410.1 (Glycine max), 3'ss of exon 2
------------------gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgcttt------agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                      ||   ||| |||    |||  ||  |  | | ||   ||| |       |  ||   |   | | ||||| ||||  |||      ||||| |||||||| || ||||||||||||||||| || || || ||||||||||| |   ||||||| || |||||||| ||||| |||||||| |||
gtcattcattttgaacaaacatgtgttattatgtcactttcaattg-cataatatagtctttatgtcgctgacatagtgatccttgttttttggtttatttttttttaagGTTTTTTTATGCCTCTAGTGCTTGTATCTATCCGGAATTCAAACAGTTGGAGACAA---ATGTGAGTTTAAAGGAGTCTGATGCCTGGCCTGCTGAG

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G36740.3 (Glycine max), 3'ss of exon 2
---------------------------------gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                                  || || |       |||| |   ||  |  | ||||    | | | |  |   |||  |   |||  |     |||||  |  ||||| |||||||| || |||||||||||||| || || || || |||||||| ||||   |||| |||||||||||||| ||||| ||||| || |||
gttagtgatggtccatatcatttcaattatatgttttgtgactaaacattttatgatgtggtgtctgttttgattatatgatgatgtgttttatgcattccaaaaaatgttt-ttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGAAACTA---ATGTTAGCTTGAAGGAGTCTGATGCATGGCCAGCTGAG

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgcttt-agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
              ||   ||  ||| ||   |  ||   |||  |   ||  | ||  |  | |     | ||| || ||||  || || |||||||| || ||||| || || || || |||||||||||| |||||||||   | ||||| ||||||||||||||||| ||||| ||||||
--------------gtagcctgtggtgtttctaagtt---gttcttcccaaggatttgga--gctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTA---ACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgcttt--agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
              ||   ||  | | ||   |  ||   |||  |   ||  | ||  |     |   | | | | |||  ||  || || |||||||| || ||||| || || || || |||||||||||| |||||||||   | ||||| ||||||||||||||||| ||||| ||||| 
--------------gtagcctgtgatgtttctaagtt---gttcttcccaaggatttggag---ctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTA---ACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ10353 (Selaginella moellendorffii), 3'ss of exon 1
gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgcttt-agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
              ||   ||  | | ||   |  ||   |||  |   ||  | ||  |  | |     | | | || ||||  || || |||||||| || ||||| || || || || |||||||||||| |||||||||   | ||||| ||||||||||||||||| ||||| ||||||
--------------gtagcctgtgatgtttctaagtt---gttcttcccaaggatttgga--gctcactctctctcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTA---ACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgcttt-agGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
              ||   ||  | | ||   |  ||   |||  |   ||  | ||  |  | |     | ||| || ||||  || || |||||||| || ||||| || || || || |||||||||||| |||||||||   | ||||| ||||||||||||||||| ||||| ||||||
--------------gtagcctgtgatgtttctaagtt---gttcttcccaaggatttgga--gctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTA---ACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG

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|125052803|gb|EL124322.1|EL124322
EST:     ATGATTAG-TTCAATATGATTGAGGCTGCTAGGATCAATGGGATTAAGAG                         GTTCTTTTATGCTTCGAGTGCTTGTA
genomic: ATGATTAGTTTCAATATGATTGAGGCTGCTAGGATCAATGGGATTAAGAGgttagttaga ... tttgctttagGTTCTTTTATGCTTCGAGTGCTTGTA
EST: gi|164162981|gb|ES187233.1|ES187233
EST:     GATTGAGGCTGCTAGGATCAATGGGATTAAGAG                         GTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
genomic: GATTGAGGCTGCTAGGATCAATGGGATTAAGAGgttagttaga ... tttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
EST: gi|125255238|gb|EL269323.1|EL269323
EST:     CTAGGATCAATGGGATTAAGAG                         GTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
genomic: CTAGGATCAATGGGATTAAGAGgttagttaga ... tttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
EST: gi|86019686|gb|DR315432.1|DR315432
EST:     CAATATGATTGAGGCTGCTAGGATCAATGGGATTAAGAG                         GTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
genomic: CAATATGATTGAGGCTGCTAGGATCAATGGGATTAAGAGgttagttaga ... tttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
EST: gi|125198826|gb|EL213780.1|EL213780
EST:     TGAGGCTGCCAGGATCAATGGGATTAAGAG                         GTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
genomic: TGAGGCTGCTAGGATCAATGGGATTAAGAGgttagttaga ... tttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
EST: gi|124716133|gb|EH807535.1|EH807535
EST:     ATTGAGGCTGCTAGGATCAATGGGATTAAGAG                         GTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGA
genomic: ATTGAGGCTGCTAGGATCAATGGGATTAAGAGgttagttaga ... tttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGA
EST: gi|116460304|gb|EG502896.1|EG502896
EST:     GATTAGTTTCAATATGATTGAGGCTGCTAGGATCAATGGGATTAAGAG                         GTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
genomic: GATTAGTTTCAATATGATTGAGGCTGCTAGGATCAATGGGATTAAGAGgttagttaga ... tttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
EST: gi|116416033|gb|EG458625.1|EG458625
EST:     ATGATTAGTTTCAATATGATTGAGGCTGCTAGGATCAATGGGATTAAGAG                         GTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA
genomic: ATGATTAGTTTCAATATGATTGAGGCTGCTAGGATCAATGGGATTAAGAGgttagttaga ... tttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                                      ttttttgtttgcttt  CT-rich tract
          tttcttaaaacaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG