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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttattgtgataccaaaagaaccctccttgttttgctttctttgttctctgtttccttacttcagaagtctcatccagtttcccgttaattagGTTACTATGGCGATTGCAAGGGAAGTTGCAGCAGTGACTCGACTTGGCATTGAG

Basic information

species Arabidopsis thaliana
transcript AT3G18680.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G15610.1 (Glycine max), 3'ss of exon 2
--------gtttattgtgata-ccaaaagaaccctccttgttttgctttct-ttgttctctgtttccttacttcagaagtctcatccagtttcccgttaattagGTTACTATGGCGATTGCAAGGGAAGTTGCAGCAGTGACTCGACTTGGCATTGAG
            |   | |||    |||  |       | ||||| ||  | |||||||| |  || || ||    || | |  |    |     | ||   || | || ||||| ||||||||||| || |||||||||||||| ||||||||||||
ataattcctgaaaacataataattgaaatgaaatgaaatattttgattcgtgttgttctcggcatcatttct--gaaattattgttttatggttggata--cagATAACCATGGCCATTGCAAGGGAGGTGGCAGCAGTGACTCGCCTTGGCATTGAG

upper sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G32340.1 (Glycine max), 3'ss of exon 2
-----gtttattgtgataccaaaagaaccctccttgttttgctttc-tttgttctctgtttccttacttcagaagtctcatccagtttcccgttaatt--agGTTACTATGGCGATTGCAAGGGAAGTTGCAGCAGTGACTCGACTTGGCATTGAG
     |||  |    | |  | ||  |        |   | ||||  | | || | |  |||   || |      ||| ||    |||   |||   |  || | || ||||| ||||||||||| || |||||||||||||| ||||||||||||
acatggttcttgaaaacataataaataaataaaacgaaatactttgatatattatgttgttctcgacattgtt--tctgattttttttttggttggatacagATAACCATGGCCATTGCAAGGGAGGTGGCAGCAGTGACTCGCCTTGGCATTGAG

upper sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0044g00890.t01 (Vitis vinifera), 3'ss of exon 3
gttt-attgtgataccaaaagaaccctccttgttttgctttctttgttctctgtttccttacttcagaagtctcatccagtttcccgttaattagGTTACTATGGCGATTGCAAGGGAAGTTGCAGCAGTGACTCGACTTGGCATTGAG
|||  | | ||| ||  || ||    |   || |  |   | | | |  ||    |   || |   ||| | ||||    | | |  | |   || |||| ||||| |||||||||||||||||| | |||||||| |||||||| |||
gttggaatatga-acataatgatatgtttatgctccgaagtatctttcttcacccttgatagtgttgaaatatcatatt-tatgctatgatacagATTACGATGGCAATTGCAAGGGAAGTTGCATCTGTGACTCGGCTTGGCATAGAG

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|124809107|gb|EH894879.1|EH894879
EST:     TTGCTGGAGACGAGGAGCAAAATATCGACCCAAAG                         GTTACTATGGCGATTGCAAGGGAAGTTGCAGCAGTGACTCGACTTGGCATT
genomic: TTGCTGGAGACGAGGAGCAAAATATCGACCCAAAGgtttattgtg ... cgttaattagGTTACTATGGCGATTGCAAGGGAAGTTGCAGCAGTGACTCGACTTGGCATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgttctctgtttccttacttcagaagtctcatccagtttcccgttaattagGTTACTATGGCGATTGCAAGGGAAGTTGCAGCAGTGACTCGACTTGGCATTGAG
               tccttac  putative branch site (score: 2)
                                        tttcccgtt  putative PPT
                                               ttaatta  TA-rich tract