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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaactttaaaatttatgcataacttagttgtctttttatagaagaccttccattttgtgattatatacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT

Basic information

species Arabidopsis thaliana
transcript AT4G04040.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 6
----------------------gtaagtaactttaaaatttatgcataacttagttgtctttttatagaagaccttccattttgtgattatatacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
                      | || | |       | | ||  | || ||     | |||    | || |  |  |  ||  |   | |     |  |||||||||| ||||||||||| ||||||||||  ||||| || || || || || ||||| ||||
taggacattttgcacataatatgaaaatcatcacggcaataata-acaagttgacgatttttcctcaaaaaagttaacgattgatccatcttctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGGAAGTACTACCACT

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------------------------------------gtaagtaactttaaaatttatgcata--acttagttgtcttt------ttatagaagaccttccattttgtgattatatacatgt-agATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
                                                                                                        |   | | ||| ||||| | ||||   ||  || ||  |||        ||     |  |  |||     |     |||  | | |||||||||| ||||||||||| ||||||||||  |||||| | ||||| ||||||||||| ||||
gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 6
-----------------gtaagtaactttaaaattt---atgcataactta-gttgtctttttatagaagaccttccat-tttgtgattatatacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
                  |   || | ||  | |||   || |||     | | |  | |    |    |   | | || ||| || | || || ||| ||||||| || ||||||||||||||||||||||| ||||| || || || |||||||| || || |
atttagttttgcatattttctatacccttttagttttagatacatggtgcatgattacatgacttgattgttttcctatgtttatgttaatgta-atgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 6
------------------gtaagtaactttaaaatttatgcata----acttagttgtctttttatagaagaccttccattttgtgattatatacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
                   | |    |||| |  ||||   | |     | |  ||   |   |  |  |       | |||| || | || |  ||| ||||||| || ||||||||||||||||||||||| ||||| || || || |||||||| || || |
attgctaaatgttatataatgatacccttttagttttacatacatggtgcatgattacatgacttgactattttcctctttttatgttaatgtg-atgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 4
----------gtaagtaactttaaaatttatgcat--aactta---gttgtctttttatagaa---gacct--tccattttgtgattatataca-tgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
           |   ||   || |  |||   | |     |||   ||||  |   |  | |    ||||   | |  ||| |  ||  ||  | || |||||||  ||||||||||||| ||||||||||| ||||| || || || |||||||| || || |
atgatttgaaatgcatattcttcagctttccccttttggattatatgttgcatgcctgcatagtctgacccagttctctttttatttgaatttaatgcagATATATGCAGAAATGATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATT

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 6
----------gtaagtaactttaaaatttatgcat--aactta---gttgtctttttatagaa---gacct--tccattttgtgattatataca-tgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
           |   ||  ||| |  |||   | |     |||   ||||  |  ||  | |    |||||  |||  ||| |  ||  ||  | || |||||||  ||||||||||||| ||||||||||| ||||| || || || |||||||| || || |
atgatttgaaatgcatatttttcagctttccccttttggattatatgttgcatgcttgcatagtctgacctagtcctctttttatttgaatttaatgcagATATATGCAGAAATGATTGGCAATGTTATGATAGATGCTCGATCAACTGGAAAATATTACCATT

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 6
---------gtaagtaact-ttaaaat-----ttatgcataacttagttgtctttttatag-aagaccttc-----cattttgtgattatatacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
         || | |||   || ||||     |||||  |    ||||    |||  || | || |   ||      || ||||  || ||  |||| |||| ||  ||||||||||||| ||||| ||||| ||||| || || || ||||||||||||||||
atcatccatgtgactaatggttgaaatgcctcttatggttgcagtagtaagttttgcattgtaaaataatcaatggtatgttgtatttttaaccatgcagATTTATGCAGAAATGATTGGGAATGTCATGATAGATGCTCGCTCAACTGGAAAATACTATCACT

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtaactttaaaatttatgcataacttagttgtctttttatagaagaccttccattttgtgattatatacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
                                 | ||  |  ||       || |   | |  |  |        |||||||||  ||||||||||||| ||  | ||| |||| || ||||| |||||||||||||| ||||
--------------------------------gtatccctcaatctttctgctgctcctctcagcctccgcg---gtagATATATGCAGAAATGATTGGGAACATCATGGTCGACGCACGTTCTACGGGAAAATACTACCACT

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|125306473|gb|EL320558.1|EL320558
EST:     CAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAG                         ATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGA
genomic: CAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCTTGCAAGgtaagtaact ... atacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacttagttgtctttttatagaagaccttccattttgtgattatatacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
 gcataac  putative branch site (score: 3)
                                attttgtgattatata  TA-rich tract