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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggtttaactccaactatcgcatagacagattccaattggcttaaaatctaattttcgagtttcttggcagGCGAATATTCGTTTCCGGCATGCCAGAAACCCCATAATCGGTGACAAGTTCAGCAGTAGACATGGGCAAAAGGGTGTTTGTTCTCAATTGTGGCCTGATA

Basic information

species Arabidopsis thaliana
transcript AT1G29940.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: LOC_Os10g35290.1 (Oryza sativa), 3'ss of exon 22
-----------------gtgaggtt----taactccaactatcgcatagacagattccaattggcttaaaatctaattttcgagt-----ttcttggcagGCGAATATTCGTTTCCGGCATGCCAGAAACCCCATAATCGGTGACAAGTTCAGCAGTAGACATGGGCAAAAGGGTGTTTGTTCTCAATTGTGGCCTGATA
                 ||  | ||    |   |  || | |    ||    | ||    |   |||   ||    ||  | | |     || ||| ||||| ||||||||| | || |  |  ||||| || ||||| ||||||||||||||||| |||||||| |||||||| |||||||| || |||||||||||||
gcatttcttgaatgttagtaggattattgtttgtgaaagtgtgttctaatttgttttttgtcatcttggcatgcttttcactactgcatgtttttgtcagGCTAATATTCGTCTGCGTCGCGTGAGAAATCCTATAATTGGTGACAAGTTCAGCAGCAGACATGGTCAAAAGGGAGTTTGTTCGCAGTTGTGGCCTGATA

upper sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM2G388892_T02 (Zea mays), 3'ss of exon 23
------------------------gtgaggtttaactccaactatcgcatagacag-attccaat-tggcttaaaatctaattttcgagtttcttggcagGCGAATATTCGTTTCCGGCATGCCAGAAACCCCATAATCGGTGACAAGTTCAGCAGTAGACATGGGCAAAAGGGTGTTTGTTCTCAATTGTGGCCTGATA
                           |  | | |  |||||  |     |      |||   || | |       | | | |      | | || ||||||||| |||||| | || | ||  |||||||| |||||||||||||||||||||||| |||||||||| ||||||||||| ||||| ||||||||||| |
cgtgcagtgagttttaaaagtactagtatttctgatgccaacagttatgaatttgttattgtgatctcgtcatgtgtttcactacttgatctttttgcagGCGAACATTCGTCTGCGTCGTGTAAGAAACCCTATAATCGGTGACAAGTTCAGCAGTCGACATGGGCAGAAGGGTGTTTGCTCTCAGTTGTGGCCTGACA

upper sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: Vv13s0084g00600.t01 (Vitis vinifera), 3'ss of exon 23
-----------------------gtgaggtttaactccaactatcgcatagacagattccaattggcttaaaatcta----attttcgagtttcttggcagGCGAATATTCGTTTCCGGCATGCCAGAAACCCCATAATCGGTGACAAGTTCAGCAGTAGACATGGGCAAAAGGGTGTTTGTTCTCAATTGTGGCCTGATA
                          |  ||  | | ||  |||    |   || || |   ||   | || |||      ||||||     |   |||||| |||||||||||| |||| | | ||||| || || || ||||| || || || || |||||||||||||| |||||||| || || |||||||| ||||
cctatgaaaatattcagcagggcacaaatttgtattacatgtattttgttt-catatgctttttacataaacatcccctatattttccttacttcgggcagGTGAATATTCGTTTTCGGCGTCCTAGAAATCCTATTATTGGTGATAAATTTAGTAGCAGACATGGGCAAAAAGGTGTTTGCTCGCAGTTGTGGCCAGATA

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|125016677|gb|EL088946.1|EL088946
EST:     TAGTTGACTTTGTCTCTGTCGACATGAAAAGCAAGAAACATCCTCAAAGG                         GCGAATATTCGTTTCCGGCATGCCAGAA
genomic: TAGTTGACTTTGTCTCTGTCGACATGAAAAGCAAGAAACATCCTCAAAGGgtgaggttta ... ttcttggcagGCGAATATTCGTTTCCGGCATGCCAGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgcatagacagattccaattggcttaaaatctaattttcgagtttcttggcagGCGAATATTCGTTTCCGGCATGCCAGAAACCCCATAATCGGTGACAAGTTCAGCAGTAGACATGGGCAAAAGGGTGTTTGTTCTCAATTGTGGCCTGATA
                              atctaat  putative branch site (score: 3)
                                            tttctt  putative PPT
                         ttaaaatctaatttt  TA-rich tract