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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgaagcagaatatatgatttagttctagctcccattgttattttgttctaaacgtctttttttctccaatgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG

Basic information

species Arabidopsis thaliana
transcript AT4G14350.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 5
------------------------------------------------------------gtcagtgaagcagaatatatgatttagttctagctcccattgttattttgttctaaacgtctttttttctccaatgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
                                                            | ||  ||   |  |||  |      ||  | |     ||   ||  |  || |||   |||  ||||    ||||   | |||||||||||||||||| ||  |||| || || | | | |||||||||||||| |||||||||||||||||||||||  ||||||| |||||||||||||| 
gtaagctcaaagctgtaaaaaaataacgtcaaatgatggtaaattttggtatgcttttatgacacggatcaatgatacttatggcggtcttcgtctggatcaataaatatttttaataatctgattttta--aatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAATCTTCAAGAA

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------gtcagtgaagcagaatatatgatttagttctagctcccattgttattttgttctaaacgtctttttttctccaatgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
                                                           | ||  ||   |  |||  |  |   ||  |       ||   || ||  ||  ||   |||  ||||    ||||   | |||||||||||||||||| ||  |||| || || | | | |||||||||||||| |||||||||||||||||||||||  ||||||| ||||| |||||||| 
gtaagctcaaagctgtaaaaaataacgtcaaatgatggtaaattttgctatacttttatgacatggatcaatgatacttattgcggtcttcttctggatcaatacttaatttcaataatctgattttta--aatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAACCTTCAAGAA

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 4
------------------------------gtca-gtgaagcagaatatat-gatttagttctagctcccattgttattttgttctaaacg------tctttttttctcca-atgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
                                || |  || |  | |||||  || |  |  | |      ||  |      |   ||| |      | || || | |  | |||   | |||||||||||||||||| ||| |||| || || | | | || ||||||||||| ||||| |||||||||||||||||| | ||||| ||||||||||| || 
gtaagctcaagcttcaaatagtcatgttacaccatgaaaatcttattatattaatcttatggtggtctttttttcttgcacatcaaaaaaggtataatattcttattttgatatgcattccagAGATATCAAGCCTGACAATTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTGGACTGCAGTAATCTTCAGGAA

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 4
-------------------------gtcagtgaagcagaatatatgatttagttctagctcccattgttattttgttc-taaacg-------------tctttttttctcca-atgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
                         || |    |  | ||| |   ||| |  |   | |    ||||| | |||  | ||||               | || |  | |  | |||   | |||||||||||||||||| ||  |||| || || | | | || ||||||||||| ||||| |||||||||||||||||| ||||||| ||||||||||| || 
gtaagctcaagctgcaaatagtcatgttacaccatgaaaatcttatattaatcttatggtggtcttgttttcttgcacataaaaaaaaaaagatataatattctaattttgatatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGTCACATGAAATTATCAGACTTTGGATTATGTAAACCACTAGACTGCAGTAATCTTCAGGAA

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtcagtgaagcagaatatatgatttagttcta-gctccc-attgttattttgttctaaacgtctttttttct-ccaatgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
              | |        | || |  ||   |  |  | ||| |  ||  | | ||       ||   |  | |   |    |  |  ||||||||||||||||| || ||| | || || || | | | || || ||||||||||||||||||||||||||||||||||| || || ||||||||||| |||
gtttgtgtaagattttatcatgattgtatgtgggaaccatatgcatgcttctgatcatgacttaagaagcaataaccctctccatatttacttattacagAGATATCAAGCCCGACAATTTACTGCTCGATAGATATGGACATATGAAATTGTCAGATTTTGGATTATGTAAACCATTGGATTGCAGTAATCTTCATGAG

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 4
gtcagtgaagcagaatatatgatttagttctagctcccattgttattttgttctaaacgtctttttttctccaatgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
                      | |  | | ||     |   |   ||     ||   || ||| | | ||   ||||   ||| |||||||||||||||||||| |||||||| ||  | || ||||||||||||||||| || || || ||||||||  |||||||   |||  | | ||  
---------------------gtatgttgcgagtcgagaacatggcttgaacttaccagtttttctgtgtcttctgtg---cagGGATATCAAGCCTGATAATCTTCTACTTGATAAGAATGGTCACATGAAATTGTCAGACTTCGGGTTGTGTAAACCCCTAGACTGCTCTAACTTACCAGCT

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|47828550|gb|CK118234.1|CK118234
EST:     GAAACTGTCCTGGCTATTGAGTCCATTCATAAGCACAACTACATTCACAG                         AGATATCAAGCCTGATAATCTGCTA
genomic: GAAACTGTCCTGGCTATTGAGTCCATTCATAAGCACAACTACATTCACAGgtcagtgaag ... tgtgatacagAGATATCAAGCCTGATAATCTGCTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagctcccattgttattttgttctaaacgtctttttttctccaatgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
                     ttctaaa  putative branch site (score: 2)
                              tctttttttctccaat  putative PPT
             ttattttgttctaaa  TA-rich tract