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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggtgttatcttttcattatctcaccttttttgtgtgttttcggcttggttatgtatctacgcatctagttcactgagctaccatataagtgtgagttataccattaagtgcgagcagcatgttctctgttttggtaacccttttaaatttttggtaattcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTTATTATCGTGCTCCAGAACTGATCTTTGGCGCCACAGAGTATACAGCATCCATAGATATAT

Basic information

species Arabidopsis thaliana
transcript AT1G06390.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 6
gtaagggtgttatcttttcattatctcaccttttttgtgtgttttcggcttggttatgtatctacgcatctagttcactgagctacca-tataagtgtgagttataccattaagtgcgagcagcatgttctctgttttggtaacc---cttttaaatttttggtaattcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTTATTATCGTGCTCCAGAACTGATCTTTGGCGCCACAGAGTATACAGCATCCATAGATATAT
                                                                              ||   ||  | | |  |  |   ||      ||  ||     |  ||| ||  || ||||   ||      |  | |  |  | ||| |   | |  ||||    |||||||| ||||||||||| || ||||| || |||||||||||||| || || || ||||| || || ||||||||| | || || || ||||
----------------------------------------------------------------------------cttggattataactgttggcctctcttccctagttctgttatttcttcat-tttgctattttaacaaatagattgatgatctccttgtactattccaccagGTTCCTGGTGAACCGAACATATCATACATTTGCTCTCGCTATTATCGTGCTCCTGAGCTCATATTTGGTGCAACCGAGTATACAACTTCAATTGACATAT

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 6
gtaagggtgttatcttttcattatctcaccttttttgtgtgttttcggcttggttatgtatctacgcatctagttcactg-agctaccatataagtgtgagttataccattaagtgcgagcagcatgttctctgttttggtaacccttttaaatttttggtaattcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTTATTATCGTGCTCCAGAACTGATCTTTGGCGCCACAGAGTATACAGCATCCATAGATATAT
                                                                       | || |||| |  |    | | |     | |     | |||  ||   || | || || | | |     ||   ||  | | ||     |  |    | | || |    |||||||| |||||||| || || ||||| |||||||||||||||||||| || || ||||| || || ||||||||| | || ||||| ||||
----------------------------------------------------------------------gaattgactgtaattcatgtgttataacaattagattctttacttgtatgctgtat-ttttttatccacata---ctaatcagttccatatgttgttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 6
gtaagggtgttatcttttcattatctcaccttttttgtgtgttttcggcttggttatgtatctacgcatctagttcactgagctaccatataagtgtgagttataccattaagtgcg-agcagcatgttctctgttttggtaacccttttaaatttttggtaattcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTTATTATCGTGCTCCAGAACTGATCTTTGGCGCCACAGAGTATACAGCATCCATAGATATAT
                                                                 | || |  || | | |  || ||  |   ||    || |    || |   |   | || || |     ||| || ||    ||||  |        |||| | ||| ||||||| |||||| ||||||| ||||| || || || ||||| ||||| ||||||||||| || ||||| || ||||| || ||||| || || ||||| |
----------------------------------------------------------------tggattt--tttattcaattatcaatttcatgaagcttctcatgttcaccacttggtaggatata----gttatgatattatttttccaca---aaaaattta-tatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCTCCAGAACTAATATTTGGTGCAACAGAATACACAGCTTCTATTGATATCT

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 6
gtaagggtgttatcttttcattatctcaccttttttgtgtgttttcggcttggttatgtatctacgcatctagttcactgagctaccatataagtgtgagttataccattaagtgcgagcagcatgttctctgttttggtaacccttttaaatttttggtaattcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTTATTATCGTGCTCCAGAACTGATCTTTGGCGCCACAGAGTATACAGCATCCATAGATATAT
                                                                 | || |  || | | |  || ||  |   ||    || |    || |   | |   ||  |      ||| || ||    |||  |         |||| | ||| ||||||| |||||| ||||||| ||||| || || || ||||| ||||| ||||||||||| || ||||| || || || || ||| | || || ||||| |
---------------------------------------------------------------gtggattt--tttattcaattatcaatttcatgaagcttctcatgttca---caacttgctaggatatagttatgatatatttttcca----caaaaaattta-tatcagGTCAAGGGTGAATCAAACATTTCATACATATGTTCACGTTACTATCGGGCTCCAGAACTAATATTTGGTGCAACTGAATACACACCTTCTATTGATATCT

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 7
gtaagggtgttatcttttcattatctcaccttttttgtgtgttttcggcttggttatgtatctacgcatctagttcactgagctaccatataagtgtgagttataccattaagtgcgagcagcatgttctctgttttggtaacccttttaaatttttggtaattcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTTATTATCGTGCTCCAGAACTGATCTTTGGCGCCACAGAGTATACAGCATCCATAGATATAT
                                                                                          |   |   | |   | | ||       |||||| || | |  ||||      ||   ||   || |||| ||   || |  |||| ||||| || || |||||||| |||||||| ||||||||||| |||||||| ||||| || ||||| || || || || ||| || |||| || || |
-------------------------------------------------------------------------------------gtgggtgcttacaaataggatccttggaattcagcagc-tgatttgcgttt------cctgctt---ttcttggcaaa--acaaacagGTGAAAGGAGAGCCCAACATATCGTATATCTGTTCCCGTTATTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

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|124711927|gb|EH803329.1|EH803329
EST:     CCTTGACCCATCAGGTTAAGCTGTGTGATTTTGGAAGTGCAAAAGTATTG                         GTCAAAGGTGAACCAAA
genomic: CCTTGACCCATCAGGTTAAGCTGTGTGATTTTGGAAGTGCAAAAGTATTGgtaagggtgt ... tcactattagGTCAAAGGTGAACCAAA
EST: gi|163987228|gb|ES045332.1|ES045332
EST:     CCTTGACCCATCAGGTTAAGCTGTGTGATTTTGGAAGTGCAAAAGTATTG                         GTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTT
genomic: CCTTGACCCATCAGGTTAAGCTGTGTGATTTTGGAAGTGCAAAAGTATTGgtaagggtgt ... tcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTT
EST: gi|125116285|gb|EL165885.1|EL165885
EST:     CTTGACCCATCAGGTTAAGCTGTGTGAATTTTGGAAGTGCAAAAGTATTG                         GTCAAAGGTGA
genomic: CTTGACCCATCAGGTTAAGCTGTGTGA-TTTTGGAAGTGCAAAAGTATTGgtaagggtgt ... tcactattagGTCAAAGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagcatgttctctgttttggtaacccttttaaatttttggtaattcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTTATTATCGTGCTCCAGAACTGATCTTTGGCGCCACAGAGTATACAGCATCCATAGATATAT
                  tggtaac  putative branch site (score: 2)
                           ttttaaatttttggta  TA-rich tract