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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcttctaagaaaacaaaagtgaaaaactgatcttcttacgttggttaatttgcaatttcgcatggtagtgtctgttctttaccaaagatgttcaccaaatgataatcttaccattgatctatatctaggacttggatgaaattttactgattatttctccatgtggttttacgtgtttcatttattcagGGTTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACCCAATGGTGCAGGGAAAACAACTACTATCAATTGTTTGACAGGCTTATTTC

Basic information

species Arabidopsis thaliana
transcript AT3G47730.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G47730.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G142249_T01 (Zea mays), 3'ss of exon 8
gtatttcttctaagaaaacaaaagtgaaaaactgatcttcttacgttggttaatttgcaatttcgcatggtagtgtctgttctttaccaaagatgttcaccaaatgataatcttaccattgatctatatctaggacttggatgaaattttactgattatttctccatgtggttttacgtgtttcatttattcagGGTTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACCCAATGGTGCAGGGAAAACAACTACTATCAATTGTTTGACAGGCTTATTTC
                                                                                                           |||  || | |||  | | |  | |  |  |  ||| || | | ||  | ||      ||      || | |    | ||||||||||| || ||| ||||  |||  || || ||  |||| ||||||||||| |||||||| || || ||||||||||| |||| |||| |||| ||  |    |
----------------------------------------------------------------------------------------------------------gtaagttttcaattagtttttgac-ataaaatacatgcaactatgcttgtcatcatctgattattcattgcctaaaac-tttattcagGGCTTATGGGTGAACCTTGAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACAC

upper sequence: AT3G47730.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G34140.2 (Glycine max), 3'ss of exon 8
gtatttcttctaagaaaacaaaagtgaaaaactgatcttcttacgttggttaatttgcaatttcgcatggtagtgtctgttctttaccaaagatgttcaccaaatgataatcttaccattgatctatatctaggacttggatgaaattttactgattatttctccatgtggttttacgtgtttcatttattcagGGTTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACCCAATGGTGCAGGGAAAACAACTACTATCAATTGTTTGACAGGCTTATTTC
                                                                                            ||||||  || ||  | || || | |     | | ||   |||  | ||   | |||    ||| ||   |  ||||| | ||  |   || ||||  ||||||||||||| ||||  |||| || ||||| ||||| |||||||| ||||||||||| || || ||||| ||  |||| ||||||||| ||||  ||  ||
---------------------------------------------------------------------------------------tctgaatgttccacatatt-tcatgtttcaacaaggcaacatggtggagattgacccattttag--gatgatgaata-atgtgctattctgaaatt-attt--tcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC

upper sequence: AT3G47730.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G20360.2 (Glycine max), 3'ss of exon 8
gtatttcttctaagaaaacaaaagtgaaaaactgatcttcttacgttggttaatttgcaatttcgcatggtagtgtctgttctttaccaaagatgttcaccaaatgataatcttaccattgatctatatctaggacttggatgaaattttactgattatttctccatgtggttttacgtgtttcatttattcagGGTTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACCCAATGGTGCAGGGAAAACAACTACTATCAATTGTTTGACAGGCTTATTTC
                                                                               | |||||  |    | ||  |  ||||    ||  ||   |    | | | | |   |||    | |||    |||| ||    | ||||| | ||  |   || ||||  ||||||||||||| ||||  |||| || ||||| ||||| |||||||| ||||||||||| || || ||||| ||  |||| ||||| ||||||||  ||  ||
-------------------------------------------------------------------------------tactttatta----ttttatctgaatg----tcccacatatttcatgtttgtggagattgacctatattaggatgatgat----caatgtgctattctgaaatt-attt--tcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGCTTGACAGGGGTAACTC

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|116447290|gb|EG489882.1|EG489882
EST:     AGTTTGGATGCTGCAAATGCGAGAAAACTTCCCCTTTTCATGCTCTGAAG                         GGTTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACC-
genomic: AGTTTGGATGCTGCAAATGCAAGAAAACTTCCCCTTTTCATGCTCTGAAGgtatttcttc ... atttattcagGGTTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACCC
EST: gi|116447291|gb|EG489883.1|EG489883
EST:     AGTTTGGATGCTGCAAATGCGAGAAAACTTCCCCTTTTCATGCTCTGAAG                         GGGTTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACC
genomic: AGTTTGGATGCTGCAAATGCAAGAAAACTTCCCCTTTTCATGCTCTGAAGgtatttcttc ... atttattcagGG-TTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgaaattttactgattatttctccatgtggttttacgtgtttcatttattcagGGTTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACCCAATGGTGCAGGGAAAACAACTACTATCAATTGTTTGACAGGCTTATTTC
          tactgat  putative branch site (score: 2)
                                         tttcattt  putative PPT
     aattttactgattatt  TA-rich tract