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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcagaggacaattgttaccatatagttaatttacatactcttgagttaaataagggatatgactatcctcctagttgacatacaatagttgtttatgctatttgttctttgtggcaattccttttacagGTGGCAGATGGTCTTGTCTTAGAGAAGACCTCATCACCATTAGGCGTACTTCTGATTGTTTTTGAATCCCGACCTGATGCACTTGTACAG

Basic information

species Arabidopsis thaliana
transcript AT2G39800.4
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39800.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------gtga-tcagaggacaattgttaccatatagttaatt-tacat--actcttgagttaaataagggatatgactatcctcctag-----ttgacatacaat--agttgtttatgctatttgttctttgtggcaattccttt-tacagGTGGCAGATGGTCTTGTCTTAGAGAAGACCTCATCACCATTAGGCGTACTTCTGATTGTTTTTGAATCCCGACCTGATGCACTTGTACAG
                                   ||| |  ||    |  |||      | |  |  || ||  |   || ||   ||    ||  ||| |   | | |    ||     ||| | |  | |  |   ||||||      ||||  |  || |  ||| |   | ||||| |||||||| ||| || |||||||||  ||||  |||||||| || || || ||||||||||| || ||||| ||||| || ||||||
gtaaagaaaggggggcttaagcatgtaatttcatatgaatttgaacttatatgtacatgcacacctggttgtatctcagctattactttctggaacagatttacattttccagcaggaatattgtccttgagttaaaacgtttatctgtgatgtttctgatgcctgttcttgcatccagGTTGCAGATGGACTTATCCTAGAGAAGATGTCATGCCCATTAGGTGTGCTCCTAATTGTTTTTGAGTCTCGACCAGATGCTCTGGTACAG
















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|116452373|gb|EG494965.1|EG494965
EST:     AGCTAGCTGATATGGAAGATCCAATCGGCCGTGTTTTAAAGAAAACAGAG                         GTGGCAGATGGTCTTGTCTTAGAGAAGACCTCATCACCATTAGGCGTACTT
genomic: AGCTAGCTGATATGGAAGATCCAATCGGCCGTGTTTTAAAGAAAACAGAGgtgatcagag ... ccttttacagGTGGCAGATGGTCTTGTCTTAGAGAAGACCTCATCACCATTAGGCGTACTT
EST: gi|86042494|gb|DR338249.1|DR338249
EST:     AGCTAGCTGATATGGAAGATCCAATCGGCCGTGTTTTAAAGAAAACAGAG                         GTGGCAGATGGTCTTGTCTTANAGAANACCTCATCACCATTAGGCGTACTT
genomic: AGCTAGCTGATATGGAAGATCCAATCGGCCGTGTTTTAAAGAAAACAGAGgtgatcagag ... ccttttacagGTGGCAGATGGTCTTGTCTTAGAGAAGACCTCATCACCATTAGGCGTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacatacaatagttgtttatgctatttgttctttgtggcaattccttttacagGTGGCAGATGGTCTTGTCTTAGAGAAGACCTCATCACCATTAGGCGTACTTCTGATTGTTTTTGAATCCCGACCTGATGCACTTGTACAG
 agttgac  putative branch site (score: 4)
                                           ttccttttac  putative PPT
     atacaata  TA-rich tract