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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctcgtccatctgctgtagcttttgttgttcttctagtttacccaatcttctgtgtataccctggctttacttgttttctagccctttctaattttgtcggtttctgcttctggtcttttccagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC

Basic information

species Arabidopsis thaliana
transcript AT1G53165.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G36130.3 (Glycine max), 3'ss of exon 8
gtatctcgtccatctgctgtag----cttttgt-tgttcttctagtttacccaatc----ttctgtgtataccctgg--ctttacttgttttctagccctttctaattttgtcggtttctgcttctggtcttttccagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC
|||| |  |  |  | ||  |     | ||| | | |||||  |||| |  | | |    |||| | ||| | |||   ||||| |  |||| |     |  |  |           ||||  ||| || || | |||||||||||||||||||| || || ||    ||||||||||||||||| || ||||| |||||||| |||||||| |||||||||||||| ||||| ||||
gtatttt-tatagttactacaaaaatcatttatgttttctttgagttcatgctaacatgtttctttttattctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgt-ttatacagGCAGATATATGGTCTCTGGGCATTACTGCAATAGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC

upper sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
---------------gtatctcgtccatctgctgtagcttttgttgttcttctagtttacccaatctt-ctgtgtataccctggctttacttgttttctagccctttctaattttgtcggtttctgcttctggtcttttccagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC
                ||       ||| |  | |   || ||   |  | |||   ||     | |     | | | || |   | |  ||||||| || ||| |   |||  |  |    ||||  ||| || || | ||||||||||| |||||||| || || ||   ||| |||||||||||||| || ||||| |||||||| |||||||| |||||||||||||| ||||| ||||
gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttt-tatcccctaagaatcatcac----tctgtatcttgt-ttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC

upper sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
---gtatctcgtccatctgctgtagcttttgttgttcttctagtttacccaatcttct-gtgtataccctggctttacttgttttctagccctttctaattttgtcggtttctgcttctggtcttttccagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC
   |||     |  |       |  |||||||| |  ||||  ||    |  | || |    | ||   |   |||  | ||  |   |   ||  ||   |  ||  |       ||||   |||| ||||||||||| |||||||| ||||| ||    || ||||||||||| || || ||||| |||||||| ||||| || |||||||||||||| || || ||||
gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttttttcacctttatttttagtttgttagtcatt--gtttttcttagaatcatcactggagtaatctg--tttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC

upper sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 8
---gtatctcgtccatctgctgtagcttttgttgttcttctagtttac-ccaatcttctgtgtataccctggctttacttgttttctagccctttctaattttgtcggtttctgcttctggtcttttccagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC
   |||     |  |       |  |||||||| |  ||||  ||    |   | |||    | ||   |   |||       |  | |   ||| ||   |  ||  |      |||||   |||| ||||||||||| |||||||| ||||| ||    || ||||||||||| || || || || |||||||| ||||| || |||||||||||||| || || ||||
gttgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgtttttccacctttattttcagtttgtgatagtcattggattttttagaatcatcactggagtattctg--tttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCGCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC

upper sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 9
gtatctcgtccatctgctgtagcttttgttgttcttctagtttacccaatcttctgtgtataccctggctttacttgttttctagccctttctaattttgtcggtttctgcttctggtcttttccagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC
           |  || |  ||  |||||  |||| ||  ||| ||  || || |||  ||    |||       || || ||  ||  |||| || || | ||    ||         |  | ||||| ||||| |||||||| ||||||||    || |||||||||||||| || ||||| ||||| || || ||||| ||||||||||||||||| || || |
---------tgaggtggt-cagtatttgtgtttctccttttttgcc--atgttttgtccat---ttgg-------tgcttcctc-ccacttctgatattattgggccatgaacaa----tgatgcagGCGGATATTTGGTCTCTGGGAATAACTGCAATTGAGATGGCAAAAGGGGAGCCTCCACTTGCAGATCTCCATCCAATGAGAGTGCTTTTTATAATACCTC

upper sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ32910 (Selaginella moellendorffii), 3'ss of exon 8
gtatctcgtccatctgctgtagcttttgttgttcttctagtttacccaatcttctgtgtataccctggctttacttgttttctagccctttctaattttgtcggtttctgcttctggtcttttc-cagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC
                                                                                | |      |||||    |  ||| |  | | |||| |   ||  ||||||||||||||||| ||||||||||| |  || || |||||||| || ||||| ||  |||| ||  | ||||| |||||||| |||||| | |||||  
-------------------------------------------------------------------------------gtatgttatgttctagcagta-cggctcattcatctgtttcattgacagGCAGATATATGGTCCCTTGGAATAACTACCATCGAAATGGCAAAGGGTGAACCGCCTTTTGCCGATTTACATCCCATGAGAGTTCTTTTTTTGATTCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgttttctagccctttctaattttgtcggtttctgcttctggtcttttccagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC
                 ttctaat  putative branch site (score: 2)
                                tttctgcttctggtct  putative PPT
                tttctaatttt  TA-rich tract