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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccattttatttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGGATGTACGTCCAAGAATTCGGTTCTGAATGCGCATTTCCCAATCAACGCC

Basic information

species Arabidopsis thaliana
transcript AT1G79000.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 8
---------------------gtaagaatgatcaaggcgtattgttgttactgtatttactgcata-tatgcgttat-----ttttctggagttcctctcg----tacaattatccttctcactcccatgccattttatttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGGATGTACGTCCAAGAATTCGGTTCTGAATGCGCATTTCCCAATCAACGCC
                      | | |    | |  || | ||| ||||| |   | ||    ||  | | ||| ||     |||| |  | |   ||  |    || |||  |  |||||  |  |||  |    |||||| | |||   |||| || ||||| || || ||||| || ||||||||||||||||| ||||| ||||||||||  ||| | ||||||  ||| || || ||||| |
gtgagaaagtggtctgatcatttgaaatatgtgatcgcctcttgatgttagtagttctaagaaattctttccgtaatgaaagttttattaaataaatcaagaaaataaaatcctaattctctttaacatttccaaatattttgc-agGCTATTCTTTTATTTCAGAAAATAGAAGGTGTGGAAGTATGCTTATTTGGCATGTATGTCCAAGAATATGGTGCAGAATGCAAATTCCCAAACCAACGTC

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 11
gtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccatt---ttatttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGGATGTACGTCCAAGAATTCGGTTCTGAATGCGCATTTCCCAATCAACGCC
                               ||  | |     |  ||   | | | |  | |   ||   || |  ||| ||   | | | |   ||||| ||   ||  | |||||||||||| |||||||||||||||| ||||| || ||||| ||| ||||||| ||||| || |||||||| || ||||||||   |||||| ||||| ||||
-------------------------------gtgatgagaaagttgatttatcaatctgatcgtaatcgaatcat-taatcatgaatattatttg-atgcccttagctttctattccagGTAGTTTTGTTGTTTCAAAAGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 9
gtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccattttatttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGGATGTACGTCCAAGAATTCGGTTCTGAATGCGCATTTCCCAATCAACGCC
                      ||  |       || | |  ||  || ||  ||| |  |  | |   |      ||   || ||| | | |||| |  | || ||||   |||||||||| |||||||||||| ||| ||||| || ||||| ||| ||||||| ||||| || |||||||| || ||||||||   |||||| ||||| ||||
----------------------gtgatgggaaagttgattttatccatccg--attgtaatcaaatcattaat---catgaatacttttgattcccttagctttctatt---ccagGTAGTTTTGTTGTTTCAAAGGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 9
gtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttatttttctggagttcctctcgtacaattatccttctcactcccatgccattttattt---ttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGGATGTACGTCCAAGAATTCGGTTCTGAATGCGCATTTCCCAATCAACGCC
                 |||  |       ||  ||||  || ||     |||  |  ||   |||   | |  |    |||| ||    | |   ||| | |||  |||   || |||||| |  |||||||||| ||||||||||| || ||||||||| | ||||| ||||| || ||||| || || ||||||||   |||||| |||||||| |
-----------------gtaaagggaaggttgc-tttagagc-tagtcatgttggtaatc--aagtcgttattat----ttattctgg--attttgatgacttttggtttccatttcagGTAATCTTGTTGTTTCAGAAGATTGAAGGTGTGGAAGTATGCCTCTTTGGCATGTATGTTCAAGAGTTTGGATCTGAATGTCAATTTCCGAATCAACGGC

upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 8
gtaagaatgatcaaggcgtattgttgttactgtatttactgcatatatgcgttat-ttttctggagttcctctcgtacaattatccttctcactccc-atgccattttatttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGGATGTACGTCCAAGAATTCGGTTCTGAATGCGCATTTCCCAATCAACGCC
                              | |      || ||||     | || |||| |    |   |  |  | | |||   |    |||    ||    ||||   |||||||||| || |||||||||| ||||||||||| |||||||||||||||||||||||||| || |||||||| || || |||||   ||| || |||||||| |
-----------------------------gtatgcaggatgtatattaagttgatgttttttcatatagttgacaaagacttaaattatgaactgaagattgtctttttcgtttccagGTAATTTTGTTGTTTCAGAAGATTGAAGGAGTAGAAGTATGCTTATTTGGGATGTATGTTCAAGAATTTGGATCAGAATGTCTATTCCCAAATCAACGTC

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|116465026|gb|EG507618.1|EG507618
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAG-CGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116428303|gb|EG470895.1|EG470895
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116462330|gb|EG504922.1|EG504922
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116447334|gb|EG489926.1|EG489926
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116414729|gb|EG457321.1|EG457321
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGAT
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGAT
EST: gi|116455250|gb|EG497842.1|EG497842
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116455249|gb|EG497841.1|EG497841
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116418401|gb|EG460993.1|EG460993
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
EST: gi|116447332|gb|EG489924.1|EG489924
EST:     AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAG                         GTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG
genomic: AAATTTTTCGGGAGGATAGTTACCCAACAGAATTTGCATACAAGTCCAAGgtaagaatga ... atttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagttcctctcgtacaattatccttctcactcccatgccattttatttttccagGTAGTTCTGTTGTTTCAAAAGATTGAAGGCGTAGAAGTATGCTTATTTGGGATGTACGTCCAAGAATTCGGTTCTGAATGCGCATTTCCCAATCAACGCC
                        ttctcac  putative branch site (score: 2)
                                      ccattttatttttcc  putative PPT
                                        attttatttttcca  TA-rich tract