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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacgatttagttgcagagtgtttgagctacctgtttacaagtgtaggctatagcccaaaatatactaaataatgatcattcttctcgtttttggatttattcagGATCTCAAACAAGAGGTTATGGTCGATCTGGTGGAGCAGTGTCGTACATACAAACAAAGAGTGGTGCACCTCGTCAACTCGACTTC

Basic information

species Arabidopsis thaliana
transcript AT4G32760.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 6
gtaacacgatttagttgcagagtgtttgagctacctgtttacaagtgtaggctatagcccaaaatatactaaataatgatcattcttctcgtttttggatttattcagGATCTCAAACAAGAGGTTATGGTCGATCTGGTGGAGCAGTGTCGTACATACAAACAAAGAGTGGTGCACCTCGTCAACTCGACTTC
   ||| ||||   |       ||||  || |   ||||  ||| || |   || ||  | | |  | |||   |    |   | |     |  |       || |||| ||| |  || ||||| || || || || ||||| || |||||| ||||||| |||||||||||||| || |||||||| || ||
---acaggattgtatgttgacatgttccagat---tgtt--caactggaccatacagttccagaagttctagtcatccctggatttctaaatagtactcaacatgcagGGTCTAAGGCAGGAGGTCATTGTGGACCTTGTGGACCAATGTCGTTCATACAAGCAAAGAGTGGTGCAGCTTGTCAACTCAACATC

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 6
---gtaacacgatttagttgcagagtgtttgagctacctgtttacaagtgtaggctatagcccaaaatatactaaataatgatcattcttctcgtttttggatttattcagGATCTCAAACAAGAGGTTATGGTCGATCTGGTGGAGCAGTGTCGTACATACAAACAAAGAGTGGTGCACCTCGTCAACTCGACTTC
   ||  ||  ||||| || || |||| |         || |||  | ||  |   ||| |  || |  ||||  | |    ||||   |  | ||  |   |   ||||||   | | ||| |||||||| || ||| |||||||||||||||| || ||||| || |||||||| ||||| |||||||| |||||
tttgtttcaacatttaatttca-agtgatca------ttgattatca-tgccgtaaataaca-aacacctacttgacatc--tcatggatgaccttggttattactttcagGGGATTAGACAGGAGGTTATTGTTGATTTGGTGGAGCAGTGTCGAACTTACAAGCAGAGAGTGGTTCACCTTGTCAACTCAACTTC

upper sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 6
gtaacacgatttagttgcagagtgtttgagctacctgtttacaagtgtaggctatagcccaaaatatactaaataatgatcattcttc-tcgtttttggatttatt--cagGATCTCAAACAAGAGGTTATGGTCGATCTGGTGGAGCAGTGTCGTACATACAAACAAAGAGTGGTGCACCTCGTCAACTCGACTTC
        ||  | |||     |  ||||| |   | ||| ||  | |  | | |   |   | |  | |   |  || ||||  |   |  ||||||   | |||  ||||  ||||  || ||||||||  | ||  |||| || |||||||| |||||||| ||||||||||| ||||| |||||||| ||| |
-------tatgcatttgtgtcatccttgaggtttttttttgcacatattagattt---ctttagttcagtctctg-tgttcatgttgggttatttttgtcctaattaacagGGGCTCAGGCAGGAGGTTATCATGGACTTGGTAGATCAGTGTCGGACATACAAGCAAAGAGTGGTCCACCTTGTCAACTCAACTGC

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|47828022|gb|CK117706.1|CK117706
EST:     TGGATGTGCTTGCGGAGATGCTGAGTGCATTAGAGCCCGGAAACAAGGAG                         GATCTCAAACAAGAGGTTATGGTCGATCTGGTGGAGCAGTGTCGTACATAC
genomic: TGGATGTGCTTGCGGAGATGCTGAGTGCATTAGAGCCCGGAAACAAGGAGgtaacacgat ... atttattcagGATCTCAAACAAGAGGTTATGGTCGATCTGGTGGAGCAGTGTCGTACATAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcccaaaatatactaaataatgatcattcttctcgtttttggatttattcagGATCTCAAACAAGAGGTTATGGTCGATCTGGTGGAGCAGTGTCGTACATACAAACAAAGAGTGGTGCACCTCGTCAACTCGACTTC
             tactaaa  putative branch site (score: 1)
                                              tttattc  putative PPT
       aaaatatactaaataa  TA-rich tract