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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacagtagcaaaatacagttttgcttttatatatgggattgaagaatgttgattaatgtgtgtttttggtttcagCTGATGGATTTGTGGTACAAACGGGAGATCCAGAGGGTCCTGCGGAAGGATTTATCGATCCAAGCACAGAGAAAACGAGGACGGTTCCTCTAGAGATTAT

Basic information

species Arabidopsis thaliana
transcript AT3G01480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G015967_T01 (Zea mays), 3'ss of exon 4
----------gtaagacagtagcaaaatacagtttt------gcttttatatat---gggattgaagaatgttgattaatgtgtgtt--tttggtttcagCTGATGGATTTGTGGTACAAACGGGAGATCCAGAGGGTCCTGCGGAAGGATTTATCGATCCAAGCACAGAGAAAACGAGGACGGTTCCTCTAGAGATTAT
             || || ||  ||  | || | ||      |   |  | |     | | | |  |||  ||   | |  ||||||  ||    | |||||||||| ||||| || ||||| |||||||||||||| || || || || ||||||||||| ||||| |  ||||   | ||||| ||||| || |||||
ttacactccatctagccattataaatgttcaatgttttagatgacctagtgtgcctagaggtcggtgaactttctctgaactgtgttggttcttatgcagCTGATGGCTTTGTTGTTCAAACTGGAGATCCAGAGGGGCCAGCTGAGGGCTTTATCGATCCCAGCACCGGCAAAATCCGTACGGTACCTCTTGAAATTAT

upper sequence: AT3G01480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0066g01410.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------gtaagacagtagcaaaatacagttttgcttttatatatgggattgaagaatgttgattaatgtgtgtttttggtttcagCTGATGGATTTGTGGTACAAACGGGAGATCCAGAGGGTCCTGCGGAAGGATTTATCGATCCAAGCACAGAGAAAACGAGGACGGTTCCTCTAGAGATTAT
                           |||     ||    | |||| |  |   || |||  |    ||  | ||     | | |  | |  |||| ||| |||||||||||||||| || ||||| |||||||| ||||||||||| || || ||||| |||||||| ||||| ||  |  |||| || || || || || ||
actactgcctccatcatgcttagttgataatttcatattgta-tacaatgctaagttgatagttttctttcgataa----aactcagatttactttttgttgcagCTGATGGATTTGTTGTTCAAACTGGAGATCCTGAGGGTCCTGCAGAGGGCTTTATTGATCCAAGTACAGAAAAGCCCCGGACAGTACCACTTGAAATCAT

upper sequence: AT3G01480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S90_50V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------gta-agacagtagcaaaatacagttttgcttttatatatg---ggattgaagaatgttgattaatgtgtgtttttggtttcagCTGATGGATTTGTGGTACAAACGGGAGATCCAGAGGGTCCTGCGGAAGGATTTATCGATCCAAGCACAGAGAAAACGAGGACGGTTCCTCTAGAGATTAT
                 ||| |||     |   |    |  | || ||| |  | ||   ||       ||| || || ||      |  |  |||||||| |||||||||||||||||||| ||||| || ||||| || || || || ||| | ||||||   || |  |||  | | || |||||  | ||||| ||
caaggtgtttggtccctgtacagatccatgagcagcttaactgtgatttcaggtttgtgtggcccttgtaatatttatcaactgtcttggtctgtttcagCGGATGGATTTGTGGTACAAACTGGAGACCCCGAGGGACCCGCTGATGGTTTTGTGGATCCAGCTACTGGCAAAGTGCGAACTGTTCCATTGGAGATCAT

upper sequence: AT3G01480.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S211_59V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------gtaagacagtagcaaaatac-agttttgcttttatatatgggattgaagaatgttgattaatgtgtgtttttggtttcagCTGATGGATTTGTGGTACAAACGGGAGATCCAGAGGGTCCTGCGGAAGGATTTATCGATCCAAGCACAGAGAAAACGAGGACGGTTCCTCTAGAGATTAT
                        || |     | || |  || |  ||||      | | |||  |       | ||||| |     | |  |  |||||||| |||||||||||||||||||| ||||| || ||||| || || ||||| ||| | || |||   || |  |||    | ||||||||  | ||||||||
attttttaatcaaggtgtctcgtctatgtagagaacatatgaccacctttggcgcggtgtgtggctt---gtgttattgatcagctgttttgctctgtttcagCGGATGGATTTGTGGTACAAACTGGAGACCCTGAGGGACCCGCTGAAGGTTTTGTAGACCCAGCTACGGGCAAAGTCCGCACGGTTCCATTGGAGATTAT

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|163976894|gb|ES086828.1|ES086828
EST:     TGTGGACTTGGTAGAGAGGCATTTCTACGATGGCATGGAGATCCAGAGAT                         CTGATGGATTTGTGGTACAAACGGGAGATCCAGAGGGT
genomic: TGTGGACTTGGTAGAGAGGCATTTCTACGATGGCATGGAGATCCAGAGATgtaagacagt ... ttggtttcagCTGATGGATTTGTGGTACAAACGGGAGATCCAGAGGGT
EST: gi|124757528|gb|EH847658.1|EH847658
EST:     TGTGGACTTGGTAGAGAGGCATTTCTACGATGGCATGGAGATCCAGAGAT                         CTGATGGATTTGTGG
genomic: TGTGGACTTGGTAGAGAGGCATTTCTACGATGGCATGGAGATCCAGAGATgtaagacagt ... ttggtttcagCTGATGGATTTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttttatatatgggattgaagaatgttgattaatgtgtgtttttggtttcagCTGATGGATTTGTGGTACAAACGGGAGATCCAGAGGGTCCTGCGGAAGGATTTATCGATCCAAGCACAGAGAAAACGAGGACGGTTCCTCTAGAGATTAT
                              gattaat  putative branch site (score: 3)
                                        tgttttt  putative PPT
     tttatatat  TA-rich tract