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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaagatataattctgtatccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G08930.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
----gcaagatataattctgtatccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataac-taattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
     | ||| | ||||    ||  || ||         |  |   |||       | || | |      | |  |     || | | || |      ||  |||||||||||||||||||| ||||| || || ||||| ||||||||     ||||  || |||| ||||| ||||| || || || |||||||||||||||
ctgtactagaaacaatttgaaat--atggatcctttccaacatccaattc---tgctgcaatcatgctggtttctttttacaactttcctattcctgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
-gcaagatataattctgtat-ccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
     ||| || ||   ||  || || |    ||   |  ||   |   |   || |  |     | || | |  | |  ||  |||| |   |   || ||||||||||||||||||||||||| ||||| ||||||||||||||   | |||| ||  |||| |||||||||||||||||||| ||||| ||||| |||
taatggatttatttaaataagcctttcatactaaatcacattaagtacttcttttcccattcttgatatttaaccattgttt--tctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 4
--------gcaagatataattctgtatccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
         ||| | |  | ||  |  |     | || | ||  |  ||   || | ||| | ||| | |      | | || |  ||  ||| || | |   || ||||||||||||||||||||||||| ||||| ||||| ||||||||   | |||||||  |||| |||||||||||||||||||| ||||| ||||| |||
taaactgtacaaaagaagaatcaattacttcccaggtca-tatttacttttatttttcatattagtgata-----ttaacaattgttt--tctttccattcaatccagATATTTGGTGGTGTTGGTATTGCTTGTCTTCCATTGGGACTTATATTTTCATTCATTCGGCGTCCAAAGGCTGTTATCACTCGTTCACAGTATATCAAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 4
-gcaagatataattctgtat-ccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
     ||| || ||  |||  || |  |    ||   |  ||            | |  |     | || | |  | |  ||  |||| |   |   || ||||||||||||||||||||||||| ||||| ||||||||||||||   | |||| ||  |||| |||||||||||||||||||| || || ||||| |||
taatggatttatttaagtaagccttccattctaaatcacattaagcgctagttgtcctattcttgatatttaaccattgttt--tctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 4
---gcaagatataattctgtatccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaat-tgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
        |||   ||||  |  | |  |    |    |  |||  ||| ||  ||||| ||  |   || |   ||||| | | |||| || | |   || ||||||||||||||||||||||||| ||||| ||||| ||||||||   | |||||||  | || |||||||||||||||||||| ||||| ||||| |||
tacttgtaataactttctaaagtcttcaatcccaggtcacatttacttt-tatttttca-tattagtgatat--caactattgttttctttccattcaatccagATATTTGGTGGTGTTGGTATTGCTTGTCTTCCATTGGGACTTATATTTTCATTCATTCGACGTCCAAAGGCTGTTATCACTCGTTCACAGTATATCAAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 3
-gcaagatataattctgtat-ccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
     ||| || ||  |||  || |  |    ||   |  ||            | |  |     | || | |  | |  ||  |||| |   |   || ||||||||||||||||||||||||| ||||| ||||||||||||||   | |||| ||  |||| |||||||||||||| ||||| || || ||||| |||
taatggatttatttaagtaagccttccattctaaatcacattaagcactagttgtcctattcttgatatttaaccattgttt--tctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATAACTCGCTCGCAGTATATCAAG

upper sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
---gcaagatataattctgtatccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaa--tatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
     | |||| ||||    |   ||    ||   ||||| |    ||| |   |||   |||||  | | |  | |||  || | |  |  |   | | || |||||||||| || ||||||||||| ||| | ||||| ||||||||   | |||||||  |||| || |||||||||||||| || ||||| ||||| |||
gagataggataaaattggaaagttat----gttt-tagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG

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|116451406|gb|EG493998.1|EG493998
EST:     CAGAATATGTTGTTGCTCTTGCGACAATTGTTGGGTCAGTTCTTTTCACG                         ATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACT
genomic: CAGAATATGTTGTTGCTCTTGCGACAATTGTTGGGTCAGTTCTTTTCACGgtatgaccat ... atatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACT
EST: gi|125025956|gb|EL098225.1|EL098225
EST:     CAGAATATGTTGTTGCTCTTGCGACAATTGTTGGGTCAGTTCTTTTCACG                         ATATTTGGTGGTGTTGGTATTGCATGTCTACCA
genomic: CAGAATATGTTGTTGCTCTTGCGACAATTGTTGGGTCAGTTCTTTTCACGgtatgaccat ... atatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCA
EST: gi|124734659|gb|EH826061.1|EH826061
EST:     CAGAATATGTTGTTGCTCTTGCAACAATTGTTGGGTCAGTTCTTTTCACG                         ATATTTGGTGGTGTTGGTATT
genomic: CAGAATATGTTGTTGCTCTTGCGACAATTGTTGGGTCAGTTCTTTTCACGgtatgaccat ... atatttctagATATTTGGTGGTGTTGGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacatttcagtaaaaaaaatctgataactaattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
                           aactaat  putative branch site (score: 2)
                                              tatttct  putative PPT
            taaaaaaaatctgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagatataattctgtatccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
-caagata
- - - - - - - - - - - - -aagtaaa
- - - - - - - - - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taactaa