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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttactcagttcttgaactctaccaaaacaaatttgacttttgagtgaaatgaaaactgagttttggcttttctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC

Basic information

species Arabidopsis thaliana
transcript AT3G02210.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
gtaagttactcagttcttgaactctaccaaaacaaatttgacttttgagtgaaatgaaaactgagttttggcttttctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
                 | |    |  ||       |||| ||||   | |  |  |  | |||         || |||||| |||      ||||||||||||||| || |||||||| ||||||||  | ||||| | | | |||||||| ||||| || |||||||||||||| ||  |||||||||||  
----------------gtaagtcatttcagtgttt-tttgtctttctggcgtcacaatta-tgacaccctttcttcctttttttgc------agTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA

upper sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
gtaagttactcagttcttgaactctaccaaaacaaatttgacttttgagtgaaatgaaaactgagttttggcttttctttttctgctgtga-------------cagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
     | |    |       |    |   |||    |   | | ||     | |   ||  | | |||||  |||| ||| |   |    |             ||||||| |||||||| || ||||||||||| || ||  | |||||||| || ||  | |||||||||||||| ||||| ||||||||  | ||||| ||   
----atcatagtggctccatatagaagttaaatttgtcaaaatcttataccata---aagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
gtaagttactcagttcttgaactctaccaaaacaaatttgacttttga--gtgaaatgaaaactgagttttggcttttctttttctgctg--------tgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
 ||||   |   ||  | |   | |   ||   |||||    |||      |  |    ||| |    |||     |||||     | |         |  ||||||| |||||||| || ||||||||||| || ||  | |||||||| || ||||| || ||||||||||| || || ||||| ||  | ||||| ||   
-taagcatc---gtgatggcgttatgagaagttaaattatgttttaagtcttataccagaaatttctctttattgattcttaacaagataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA

upper sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
gtaagt-tactcagttcttgaactctaccaaaacaaatttgacttttgagtgaaat-----gaaaactgagttttggcttttctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
 |||    |   ||| || | |      | | |||| ||  |||||||  |  | |     | | |  | ||| |           ||||       ||||||| |||||||| || |||||||| || || ||  | |||||||| || ||| | |||||||||||||| ||||||||||||||  | ||||| ||   
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA

upper sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
-gtaagttac--tcagttcttgaactctaccaaaacaaatttgacttttgagtgaaatg---aaaactgagttttggcttttctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
    | | ||    |||  | | |   |  | | |||| ||  | ||| |  |  | |    |  ||||||  ||           ||||       ||||||| |||||||| || |||||||| || || ||  | |||||||| || ||| | |||||||||||||| ||||| ||||||||  | ||||| ||   
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
-----gtaagttactca--gttcttgaactctaccaaaacaaatttgacttttgagtgaaatgaaaactgagttttggcttttctttttctgctgt-gacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
      |   |||  ||  ||||    |   ||  |  |  ||    |  ||| |||    |  | | |  |||| |  |  |||   | |  | | | ||||||| |||||||| || |||||||| || || ||| | |||||||| || |||||||||||||| ||||| ||||| || |||||||| ||| ||||   
tatttatgctttatacattgttcagataaattattagtatgaaaaccatgttttagttt--ttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA

upper sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
----gtaagttactcagttcttgaactctaccaa-aacaaatttgacttttgagtgaaatgaaaactgagttttggcttt--tctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
     ||| ||    |     ||||   |||       |  | | ||| |    | |    |  | |  ||| |  | ||    |   |    | |  ||||||| |||||||| || ||||||||||| || ||  | ||||||||||| ||  |||||||||| || |||||||| || |||||  | ||  | ||| |
gtgcttaaatt-taaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
------gtaagttactcagttcttgaactctaccaaaacaaatttgacttttg--agtgaaatgaa--aactgagttttggcttttctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
      | ||      ||  |    |  | | |  |      |||   |  |   ||  | ||  |  |||| |||||   |  ||  | |  |  | || ||||||| ||||||||||| |||||||| || || ||  | ||||||| |||||| | |||||| || || |||||||| || |||||| | ||  | ||  |
ttatccgaaaagggtccaagttaacagttgttctgagtt---tttagttcctactagcaagatccatcaacttagtttgacccattgctctgat-ttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttttgagtgaaatgaaaactgagttttggcttttctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
 atttgac  putative branch site (score: 4)
                          ttttggcttttctttt  putative PPT
                                 ttttcttttt  TA-rich tract