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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtactcaatcttcattgtccctatttcattatctggtttgtgagaaaatctaacaattgagtttgggttctcatggaaggacaacacttacatattctatttttcaattttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACGATTGTCACAGTAGCCAAATGGGGCCGTTCTGTGTACATAAATATTCAGA

Basic information

species Arabidopsis thaliana
transcript AT1G27770.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 4
gtgtgtactcaatcttcattgtcccta-tttcattatctggtttgtgagaaaatctaacaattgagtttgggttctcatggaaggacaacacttacatattctatttttcaattttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACGATTGTCACAGTAGCCAAATGGGGCCGTTCTGTGTACATAAATATTCAGA
           |  ||  |||||   | ||  | || |   |   |   |    || | | ||   |     || |||        | | | || |  | | |  | |      || | ||||||||||||||||||| || |||||||| || || || |||||||| || || ||||| || || |||||||| || || |||||||| ||||||||||
-----------aatttagttgtcttgagttgtactacc--atccatttcatgccctcatagttctatgcactttttcactc-----ccaaaatttctcactgtgctatctg---tttgcagGTGGCAAAAGAAAGTGCTGACGTGATTATTCTTGACGACAACTTCTCCACTATAGTCACTGTTGCTAAATGGGGTCGGTCAGTGTACATTAATATTCAGA

upper sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 4
gtgtgtactcaatcttcattgtccctatttcattatctggtttgtgagaaaatctaacaattgagtttgggttctcatggaaggacaacacttacatattctatttttcaattttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACGATTGTCACAGTAGCCAAATGGGGCCGTTCTGTGTACATAAATATTCAGA
                  | ||  |||    |     ||||   ||     || |   |    |  |||   |       |      | |||| | | || | |||||          |||| |||||||||||||| ||||| || || |||||||||||||| || || ||||| || ||||||||||||||||| || || |||||||| |||||||
------------------tggttgctagcagaggtcttggtccttggagttat-tgttatgccaaattgtacttgatgatatattttatactt-cttttttttttttttgtcaaattcagGTAGCAAAAGAAAGTGCCGATGTAATAATTCTAGATGATAACTTTTCAACTATTGTAACTGTAGCCAAATGGGGCCGCTCGGTCTACATAAACATTCAGA

upper sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G04900.1 (Glycine max), 3'ss of exon 4
gtgtgtactcaatcttcatt-gtccctatttcattatctggtttgtgagaaaatctaacaattgagtttgggttctcatggaaggacaacacttacatattctatttttcaattttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACGATTGTCACAGTAGCCAAATGGGGCCGTTCTGTGTACATAAATATTCAGA
              |||||| ||  |||    |     || ||  ||     ||          | ||  |    | |||  |     | |||      || | ||| |||||||    |||| ||||||||||| || ||||| || || |||||||||||||| || || ||||| || ||||| ||||||||||| || || ||| |||| |||||||
-------------tttcattagttgctagcagagatcttgattcttggacttattcttatgccaaatt--gtacttgatgatatatttatactcct---ttttttttgtcaatttc---agGTAGCAAAAGAAAGCGCTGATGTAATAATTCTAGATGATAACTTTTCGACTATTGTGACTGTAGCTAAATGGGGCCGCTCGGTCTACGTAAACATTCAGA

upper sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S37_351V6.1 (Physcomitrella patens), 3'ss of exon 6
gtgtgtactcaatcttcattgtccctatttcattatctggtttgtgagaaaatctaacaattgagtttgggttctcatggaaggacaacacttacatattctatttttcaattttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACGATTGTCACAGTAGCCAAATGGGGCCGTTCTGTGTACATAAATATTCAGA
     | || | |||    |||   ||| |    | |||  | | ||           | || | | |||||| | |     |   | |      | |||  | || |     |||  |||| || || |||||||| |||||| |||| || || ||||| |||||||| ||||||   || ||||| ||||| ||||||||||| | ||| ||||| |
----ttgcttattctgtggtgtagatatcttcccaactgtctaggga-----------agttaaatctgggttgtgacccgtgctgatc-----tacattgaacttattgtgattctcagGTTGCTAAGGAAAGTGCAGATGTGGTTATACTGGACGATAATTTCTCTACCATTGTCGTTGTGGCCAAGTGGGGTCGTTCTGTGTATACAAACATTCAAA

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|116432622|gb|EG475214.1|EG475214
EST:     CACTTCATGAAGCTGATATTGGACTCGCAATGGGCATTTCCGGAACTGAG                         GTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACG
genomic: CACTTCATGAAGCTGATATTGGACTCGCAATGGGCATTTCCGGAACTGAGgtgtgtactc ... attttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACG
EST: gi|116441411|gb|EG484003.1|EG484003
EST:     CACTTCATGAAGCTGATATTGGACTCGCAATGGGCATTTCCGGAACTGAG                         GTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACG
genomic: CACTTCATGAAGCTGATATTGGACTCGCAATGGGCATTTCCGGAACTGAGgtgtgtactc ... attttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACG
EST: gi|86059592|gb|DR355349.1|DR355349
EST:     CACTTCATGAAGCTGATATTGGACTCGCAATGGGCATTTCCGGAACTGAG                         GTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACG
genomic: CACTTCATGAAGCTGATATTGGACTCGCAATGGGCATTTCCGGAACTGAGgtgtgtactc ... attttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgggttctcatggaaggacaacacttacatattctatttttcaattttcgtagGTGGCAAAAGAAAGTGCGGATGTGATTATCCTAGATGATAACTTCTCTACGATTGTCACAGTAGCCAAATGGGGCCGTTCTGTGTACATAAATATTCAGA
                       cacttac  putative branch site (score: 2)
                                              ttttcgt  putative PPT
                          ttacatattctatttt  TA-rich tract