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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtttattcagGTAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCTCTCTTCCCCTTTTTGTGCTTCGGAATTGGCTTTCTCCTAAACACAATTGCCATATTCTATGG

Basic information

species Arabidopsis thaliana
transcript AT1G10950.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 9
--------------------------------------gtatgacttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtttattcagGTAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCTCTCTTCCCCTTTTTGTGCTTCGGAATTGGCTTTCTCCTAAACACAATTGCCATATTCTATGG
                                      |||||  |   | |  ||| |  |  | ||   | ||  |||  |   | | |||  || || |||  ||    |||| || ||||||||| ||||| || | |||| | || || |||||||| ||||| ||  ||||||| |||||||| ||| || |||||||||| || |||||||||||
gtaagaatcttctttaattttctgtattttcgctcctagtatgtttgggtggctttgtctcagtcttctccttttggttt--tgaatgattatgtaactattttttatct--gtttgtt-agGTAAACACTGGATTAAATCCATGATTCTTACTGCTTCTCTGTTCCCATTCATGTGCTTTGGAATTGGATTTATCTTAAACACAATCGCTATATTCTATGG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 9
--------------------------------------gtatgacttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtttattcagGTAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCTCTCTTCCCCTTTTTGTGCTTCGGAATTGGCTTTCTCCTAAACACAATTGCCATATTCTATGG
                                      |||||  |   | |  ||| |  |  | ||   | ||  |||  |   | | ||| ||| ||||||  ||| | |||     ||||||||| ||||| || | |||| |||| || |||||||| ||||| ||  ||||||| |||||||| ||| |  |||||||||| || |||||||||||
gtaagtatcttctttaattttctgtatattcgctccaagtatgtttgggtggctttgtctcagtcttctctttttggttt--tgaatgattatgcaactaatttttatgtttgtt-----agGTAAACACTGGATTAAATCCATGATCCTTACAGCTTCTCTGTTCCCATTCATGTGCTTTGGAATTGGATTTATATTAAACACAATCGCTATATTCTATGG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 9
gtatga-cttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtt----tattcagGTAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCTCTCTTCCCCTTTTTGTGCTTCGGAATTGGCTTTCTCCTAAACACAATTGCCATATTCTATGG
||| ||  || |     |    |   |      || ||   | | |||||  |  |   | | |||  ||   || ||    | |||||||||| ||||||| || | |||| |||| || || || || ||||| ||  ||||||| |||||||| ||| |  ||||||||||||| |||||||||||
gtaagaatttgcattgatctttgctacatgtttgt-ttgggtgcttctctctccctctgaatgattataaccgtgcttataattttcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCATGTGCTTTGGAATTGGTTTTATTTTAAACACAATTGCTATATTCTATGG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 9
-----------------gtatgacttactcgacttggcggacccctccagtgttactttc---ctctctaactattcaagtaatttaaatgctggtt----tattcagGTAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCTCTCTTCCCCTTTTTGTGCTTCGGAATTGGCTTTCTCCTAAACACAATTGCCATATTCTATGG
                  ||||    |       | |  |     |   |||   || ||   ||||||  || |   | | |||   |   || ||    | |||||||||| ||||||| || | |||| |||| || || || || ||||| ||  ||||||| |||||||| ||| |  ||||||| ||||| |||||||||||
gtaagattcgcattgatctatgctacatgttctcttgatgtttgtttaggtgcctctctctctctctctctctctctgaatgattatgactgtgcttatcattttcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCTTTCATGTGCTTTGGAATTGGTTTTATTTTAAACACTATTGCTATATTCTATGG

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|164197654|gb|ES142568.1|ES142568
EST:     TTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGG                         GTAAACATTGGATCAAGTGCATGGTCC
genomic: TTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgactta ... gtttattcagGTAAACATTGGATCAAGTGCATGGTCC
EST: gi|125284758|gb|EL298843.1|EL298843
EST:     TTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGG                         -TAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCT
genomic: TTCTTTTGTCTCTGGTTATGTGAGCGGTGGAATGTACTCAAGAAGCGGGGgtatgactta ... gtttattcagGTAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagtgttactttcctctctaactattcaagtaatttaaatgctggtttattcagGTAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCTCTCTTCCCCTTTTTGTGCTTCGGAATTGGCTTTCTCCTAAACACAATTGCCATATTCTATGG
                ctctaac  putative branch site (score: 2)
                                              tttattc  putative PPT
                   taactattcaagtaat  TA-rich tract