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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatatagaaatcttatgctattttgactccaaattaacttctggattttaacaattattatgctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA

Basic information

species Arabidopsis thaliana
transcript AT1G02890.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
--gtaattatatagaaatc-ttatgctattt--tgactcc--aaattaacttctggattttaacaattattatgctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA
    |||    || | ||     |||| |||  ||| |||   | |||  | ||| |   |  | | |   | |   | || | |||||||||||| |||||||||||||| |||||||  ||  |    || || || || || | ||| || || ||| | ||   ||||||||| || ||||| |
gtacaatcccctacatattgccgtgctttttggtgattcctcgagttatttactgaacact--ctacttacaagtcctttt-tctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA

upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 16
-------------------gtaattatatagaaatcttatgctattttgactccaaattaacttctggattttaacaattattat-gctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA
                    || |   | | || | ||  || ||  ||  | |         | |  | | |||   ||   || |   | || |  |||||||| ||||| ||||||||||| ||||||||||||||  | || || ||||| || | |||||| || ||  | ||   ||||||||| ||||| ||||
aagattaagatattttcgtatattctaacacaagtatttagc-atactggtttctctagtttatttacactgtaatggtttgaattgaattgttttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 15
---------------------------------------------------------------------------gtaattatatagaaatcttatgctattttgactccaaattaacttctggattttaacaattattatgcta--tattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA
                                                                           |||   || |||     |||   | |  ||| |     | || |   | ||| | ||   |||| |   |  | || || |||||||| ||||| ||||||||||| ||||||||||| ||  | || || ||||| ||||  ||||| || ||  | ||   ||||||||| ||||| ||||
gtaatttaatattagatgttacaattataaacctttctccatcatattttgtggagatattttgcattactactggtatccatctagtttctttaccttgtcatgatt-----tgaattgtggaattgtcacctgtattctttgaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCGCCAACCGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
---------------------------------------------------------------------gtaattatatagaaatc-ttatgctattttgactccaaattaacttctggattttaacaattattat--gctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA
                                                                      || |  |||  |  |  ||    ||  ||| |      | || |   ||||| | ||   |||| |  |   | || || |||||||| ||||| ||||||||||| ||||||||||| ||  | || || ||||| |||| |||||| || ||  | ||   ||||||||| ||||| ||||
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 16
-------------------gtaattatatagaaatcttatgctattttgactccaaattaacttctggattttaacaattattatgctatattattt---cagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA
                    || |   | | || | ||  || ||  ||  | |    |   || |  |   |   |    ||    |  ||| |||   ||||| || ||||| ||||||||||| ||||||||||||||  | || || ||||| || | |||||| || ||  | ||    |||||||| ||||| ||||
aagattaagatatttttgtatattctaacacaagtattcagc-atgctggtttct--ctggtttatttacactggaatggtttgaattgaattgtttgcccagGACGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGACGATATTGGAGCTTTAGAAA

upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
------------------------------------gtaattatatagaaatcttatg---ctattttgactccaaattaactt--ctggattttaacaattattatgctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA
                                     |  |   | | ||| || |       ||   | ||   || | | ||      || ||   |||| |||||| | | | ||||||||||| ||||| ||||||||||| ||||| ||||| || ||||| || ||||| || |||||||| || ||  ||||   ||||||||| ||||| ||||
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttgg-aatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA

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|86059541|gb|DR355298.1|DR355298
EST:     TGTTGCATGAGATTCAAAACGAAAACAAGAGCACAAAGAAATCTCTGAAA                         GATGTTGTTACAGAGAATGAATTCGAGAAAAA-CTACTATCAGACGTCATT
genomic: TGTTGCATGAGATTCAAAACGAAAACAAGAGCACAAAGAAATCTCTGAAAgtaattatat ... attatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgactccaaattaacttctggattttaacaattattatgctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA
                        ttttaac  putative branch site (score: 2)
                                              ttatttc  putative PPT
                       attttaacaattatta  TA-rich tract