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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttataacaaatcctcttacttgtttctagctttggtcttaaacctcttggttatcttatttggggattctagtggcaacactcattatttcctttttcatcgctgagttccttttttggtcacggttagaagatgtacggtgaagctaattactcccatccttttcttttttctagGTCCTTGCTGATAGGATTAATCTCCCATGTATGCTGGTAAAAGGCAGTTACTACACTGGAACTGATGATGGGGCTGTGAACTTGATTAAACTAGATGACA

Basic information

species Arabidopsis thaliana
transcript AT5G11850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G34730.1 (Glycine max), 3'ss of exon 2
gtttataacaaatcctcttacttgtttctagctttggtcttaaacctcttggttatcttatttggggattctagtggcaacactcattatttcctttttcatcgctgagttccttttttggtcacggttagaagatgtacggtgaagctaattactcccatccttttcttttttctagGTCCTTGCTGATAGGATTAATCTCCCATGTATGCTGGTAAAAGGCAGTTACTACACTGGAACTGATGATGGGGCTGTGAACTTGATTAAACTAGATGACA
                                                                  |  | ||||   |       |||  | |  |||||  | ||   ||    |   |  |   |||   ||| |    | |||||||   || |  ||   ||||  |   ||||| |||||||||||||||||  | || || | |||||||||||| || || || |||||||||||||||||||||||||| |||||||||  ||||||  
---------------------------------------------------------------aaagcatttagttata-----tgttaccttcaatttcaaagttgg--tcaggctcatgcaat--ttatttgatttcaactaaagctaa---cttcagtc---ttctggtgcttagGTACTTGCTGATAGGATTAACGTTCCCTGCAAGCTGGTAAAAGGGAGCTATTATACTGGAACTGATGATGGGGCTGTGAATTTGATTAAAGCAGATGATG

upper sequence: AT5G11850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G10790.2 (Glycine max), 3'ss of exon 2
gtttataacaaatcctcttacttgtttctagctttggtcttaaacctcttggttatcttatttggggattctagtggcaacactcattatttcctttttcatcgctgagttccttttttggtcacggttagaagatgtacggtgaagctaattactcccatcctt----ttcttttttctagGTCCTTGCTGATAGGATTAATCTCCCATGTATGCTGGTAAAAGGCAGTTACTACACTGGAACTGATGATGGGGCTGTGAACTTGATTAAACTAGATGACA
                                                                                 |  ||||   | || | | | |  | | || |    ||||||| | | |    || ||   |||    || ||   | | | |     ||||  |   ||||| |||||||||||||||||  | || || |||||||||||||| || || || ||||||||||| ||||| |||||||| |||||||||  ||||||  
--------------------------------------------------------------------------------aaagcatttagttctatgttacc-ttcaatttcaaagttggtcaggttcatgcaatttatt-tgatttcaactaaagctaacttcagtcttctggtgcttagGTACTTGCTGATAGGATTAACATTCCCTGCATGCTGGTAAAAGGGAGCTATTATACTGGAACTGACGATGGTGCTGTGAATTTGATTAAAGCAGATGATG

upper sequence: AT5G11850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0008g01310.t01 (Vitis vinifera), 3'ss of exon 2
gtttataacaaatcctcttacttgtttctagctttggtcttaaacctcttggttatcttatttggggattctagtggcaacactcattatttcctttttcatcgctgagttccttttttggtcacggttagaagatgtacggtgaagctaattactcccatccttttcttttttctagGTCCTTGCTGATAGGATTAATCTCCCATGTATGCTGGTAAAAGGCAGTTACTACACTGGAACTGATGATGGGGCTGTGAACTTGATTAAACTAGATGACA
                                                                    | |||     ||  |     |  |  || | | ||  | |      ||||| ||   | |||    ||      ||||| |||||  || ||| ||   | |  | |||||| || ||||||||||||||||| |||||| ||||||| ||||| || |||||||| || |||||||| |||||  | ||| |||||||| | ||| |  
--------------------------------------------------------------------tgctaac--taatgccttagagataattctacttcttttaaaagtattttttgtt-tgattaa---attctaactgaagttaattg-tctcatgct---cctggtgctagGTGCTAGCTGATAGGATTAATCTTCCATGTCTGCTGGTTAAAGGGAGCTACTACACGGGTACTGATGACGGGGCCATAAACCTGATTAAAATTGATAATG

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|116416001|gb|EG458593.1|EG458593
EST:     TTGGTCGAGTTAATGTTGGTCTTGCACGACACAGGGCTTTGCTTTTCAAG                         GTCCTTGCTGATAGGATTAATCTCCCATGTATGCTGGTAAAAGGCAGTTAC
genomic: TTGGTCGAGTTAATGTTGGTCTTGCACGACACAGGGCTTTGCTTTTCAAGgtttataaca ... ttttttctagGTCCTTGCTGATAGGATTAATCTCCCATGTATGCTGGTAAAAGGCAGTTAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggttagaagatgtacggtgaagctaattactcccatccttttcttttttctagGTCCTTGCTGATAGGATTAATCTCCCATGTATGCTGGTAAAAGGCAGTTACTACACTGGAACTGATGATGGGGCTGTGAACTTGATTAAACTAGATGACA
                      agctaat  putative branch site (score: 3)
                        ctaattactcccatcc  CT-rich tract
                                        ttttcttttttcta  TA-rich tract