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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatataagttctatctcccttccactacttactccttattgtagtgaaccattttgcctaactaaagatgaatttttgtttggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCTGCAATGATCCAGCTTGAATTACCACATGTCAACATCCTCTCAAAAATGG

Basic information

species Arabidopsis thaliana
transcript AT4G12790.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G12790.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 6
gtatta--tataagttctatctcccttccactacttactccttattgtagtgaaccattttgcctaactaaagatgaatttttgtttggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCTGCAATGATCCAGCTTGAATTACCACATGTCAACATCCTCTCAAAAATGG
|| | |   || | |   |  |  |||     | | |     ||||| |   ||  |    |||| | ||    ||  |||||   ||   |||||  |||  |||||||| || |  ||||||||||||||| | |||||  |||| ||||| ||||||||| | || ||| |||||||||| ||||| ||||
gtttgaatcatgaatataaattttctt--gtcaatgaagatatattgaaccaaaa-accaagcctgagtacgtttg--ttttttcatgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGG

upper sequence: AT4G12790.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G154716_T01 (Zea mays), 3'ss of exon 8
gtattatataagttctatctcccttccactacttactccttattgtagtgaaccattttgcctaactaaagatgaatttttgtttggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCTGCAATGATCCAGCTTGAATTACCACATGTCAACATCCTCTCAAAAATGG
|| | |   | |           |      | | | |   ||||| |   || |     |||  | ||  | |  ||||||   ||   |||||  |||  |||||||| || |  || |||||||||||| | |||||  |||| ||||| ||||||||| | || ||| |||||||||| ||||| ||||
gtttgaatcatgaatagaaattttcttgacaatgaatatatattgaaccaaaac-ccaagcccgagtacggtt--attttttcatgatccagTTTGTCAGCGATGTAACAAAATACATTAGTGGTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGG

upper sequence: AT4G12790.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G39880.1 (Glycine max), 3'ss of exon 6
---------------------------------gtattatataagttctatctcccttccactacttactccttattgtag----tga--accattttgcctaactaaagatgaatttttgtttggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCTGCAATGATCCAGCTTGAATTACCACATGTCAACATCCTCTCAAAAATGG
                                  ||   |||  | ||| ||    | | |     | |   ||||||||     | |  |  || ||   | |||  |     |||    | |    |||||||| ||||| || ||||||||||| ||||| |||||| ||| |||  |||| ||| | || |||||| |||| ||||| || ||||||||||| ||||
gtttgtggtagtttgttgagaaaatattttcttttaagttattggctctctcatattcctatagacttcctgttattgtatattttaattattatctttgttgactctaataatattaaaatgttttccagTTCATGACAGACGTGACCAAGTTTATAAGTGGATGCATGGCATGTCTTTCTGCGATGGTTCAACTTGAACTACCTCATGTTAATATCCTCTCAAAGATGG

upper sequence: AT4G12790.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 3'ss of exon 5
gtattatataagttctatctcccttccactacttactccttattgtagtgaaccatt-ttgccta-actaaagatgaatttttgttt--------------ggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCTGCAATGATCCAGCTTGAATTACCACATGTCAACATCCTCTCAAAAATGG
    | | ||   | | ||||||||   | |     |  ||||| || |||    || |||| |  | | |   |   ||||| |||                |||||||||| |||||||| |||||||| || |||||||||||| |||||||  |||||||| |||| || ||||| || ||||| || || ||||| |||||||
---gtttgtagaattt-tctcccttgggc-ataattttattattttaatgactggttattgcttgtattgagagttcttttttttttcttcttcctttttaatatcagTTCATGACAGATGTTACCAAGTTCATTAGTGGTTGCATGGCATCTCTTTCTGCAATGGTCCAACTCGAATTGCCTCATGTTAATATTCTCTCCAAAATGG

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|124951233|gb|EL026623.1|EL026623
EST:     AAGAACTTCAACGTCTGTGTTGTTTATCTGCTTGATTCACAG                         TTCATCACAGATGTAACCAAGTTTATCAGTGGTT
genomic: AAGAACTTCAACGTCTGTGTTGTTTATCTGCTTGATTCACAGgtattatata ... tttggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTT
EST: gi|86085798|gb|DR381557.1|DR381557
EST:     TGAAGCAGAAGAACTTCAACGTCTGTGTTGTTTATCTGCTTGATTCACAG                         TTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCT
genomic: TGAAGCAGAAGAACTTCAACGTCTGTGTTGTTTATCTGCTTGATTCACAGgtattatata ... tttggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCT
EST: gi|164236440|gb|ES191059.1|ES191059
EST:     GAAGAACTTCAACGTCTGTGTTGTTTATCTGCTTGATTCACAG                         TTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTC
genomic: GAAGAACTTCAACGTCTGTGTTGTTTATCTGCTTGATTCACAGgtattatata ... tttggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTC
EST: gi|301501514|gb|HO207054.1|HO207054
EST:     TGAAGCAGAAGAACTTCAACGTCTGTGTTGTTTATCTGCTTGATTCACAG                         TTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCT
genomic: TGAAGCAGAAGAACTTCAACGTCTGTGTTGTTTATCTGCTTGATTCACAGgtattatata ... tttggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttattgtagtgaaccattttgcctaactaaagatgaatttttgtttggatcagTTCATCACAGATGTAACCAAGTTTATCAGTGGTTGCATGTCATCTCTCGCTGCAATGATCCAGCTTGAATTACCACATGTCAACATCCTCTCAAAAATGG
                          aactaaa  putative branch site (score: 2)
                                       tttttgttt  putative PPT
                             taaagatgaattttt  TA-rich tract