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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT

Basic information

species Arabidopsis thaliana
transcript AT1G79990.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 11
--ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
   |||    |||  |      | | ||     |   ||  ||  || |   |      |  ||  |  || || ||||   | |  |||||| ||  ||||||||| ||||| ||||| ||||| || ||||| |||||||||||||||||||| |  || || || ||||| ||||| ||| | |||||||||||||| |
ggctac-aacatttcttttctttct-actaggtaatgttagttgtttgtcatatcttgaatagtattcaatcttactatgtgtcatctttttgtttggtcagAGCTTAAAGCATAACCCCAATGGAAGATTTGTCGTAGTTTGTGGAGATGGTGAATTCATAATTTATACTGCATTGGCTTGGAGGAATAGGTCATTTGGAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
---ttactggtattagtaaga--aatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
   |   | ||  |||||| |  ||  | | || |||||   |||      ||| | ||     | |  ||  |  || || || |||   | |     ||||||||||| | |||||| || ||||| || ||||| || || ||||||||||| || || || ||||||||||| || || ||| ||||||| ||||| || |
gattctgttgttgtagtaaaattaaattaatctcaaatctagtatag----tgtaattatagtgtat-gttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 10
------------------------------------------ttactggtattagtaagaaatatgaccttaaat----catttattaattttgtgac-------tacccact----gtcatttatgtttctattat--ttaat--tttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
                                          |||||  | |  ||    | | ||   || ||     ||| | ||  |||| | |        | | || |    ||    |||  |   ||| |  |||||  |||||| ||  ||||||||||||||| || ||||||||  |||| || || || ||||||||||||||||| || || || |||||| |||| ||| | |||||||||||||| |
gtacttttggatgctgatgtgttctttgtattttaaaacttgttactattgtaggtttatagtgtggtttttaagtggacatcttttcgttttattatttggtggtgctcattttgtgtggcgtataatctgattgtgattaattatttttggttggtcagAGCTTGAAGCATAATCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGTGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGGTCATTTGGAT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 11
ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatt--taatt-ttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
   ||    |       |   |||        ||    |     | ||   ||     | || || |||  |   ||| |   ||||  ||||| ||  ||||||||||||||| |||||||||||  |||| || || || ||||||||||| ||||| || || || |||||| |||| ||| | ||||| |||||||| |
--ccttccctagaccccacccatgcggaagcctctggcaccgggtctgcc-cttttttcagtaatgtataatctgattgtgagtaatcattttggttggtcagAGCTTGAAGCATAACCCTAATGGACGGTTCGTTGTTGTATGTGGAGATGGCGAGTACATAATTTATACTGCCCTGGCCTGGAGGAATAGATCATTTGGGT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
ttactggtattagtaagaaatatgaccttaaatcatttattaatt-ttgtgactacccactgtcatttatgtt--tctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
  |   ||     | | ||  ||   | | | |  |   | |||| |    | ||     | ||||   || |    |||| || | ||  ||  || | ||||  || |||||||| || ||||| |||||||| || || ||||||||||||||||| ||||| |||||||| ||||| ||| |||||||||||||||| |
--agaagtgagttttaaaacaatagtccttattgctggttcaattatcaacaatatttgtt-tcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtt--tctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
  |   |  ||   ||  |||| | |||||   |   |   | | |    | ||     | | ||   || |     ||| || | ||  ||  || | ||||  || |||||||| || ||||| |||||||| || || ||||||||||||||||| ||||| |||||||| ||||| ||| |||||||||||||||| |
agaagtgagttttaaaataata-gtccttattgcgggttcaattatcagcaatatttgtt-ttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
ttactggtattagtaagaaatatgaccttaa--atcatttattaattttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
 ||    || || |        |    ||||  ||||    ||| || | |    |  ||   | | |  ||| |   || |    |  |||  |  |  |||| || | |||||| || ||||| |||||||| || |||||||||||||| ||||||||||| |||||||  ||||| ||| ||||||| |||||||| |
-taa-aataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
---ttactggtattagtaagaaatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
   ||     || || |  |     |    |||| | ||||   | |||| |   ||  ||   | | |  ||| |   || |  | ||  ||   || ||||||  | | |||||| || ||||| ||||| || || |||||||||||||| || |||||||| |||||||| ||||| ||| ||||||| |||||||| |
agctttaaaataataatctgccccttagttttaa-ttattt-ccacttttttttttaagcatgttgactggtgtctgacttgtg-atttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
ttactggtattag--taagaaatatgacc--ttaaatcatttattaattttgtgac-tacccactgtcatttatgt-ttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
      | ||||   || ||   ||||    ||  | ||| | |||||||  ||   |      |  ||||||| | |||  || |||  ||||||  | ||||||||| | || || ||||| ||||| |||||||| || |||||||||||||||||||| ||||| || || || ||||| ||| | |||||||| ||||| |
------gcattaagctaggatgaatgattgtttccaccatattttaatttattgttatttatgtttacatttatttcttccttttttttttttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 11
-ttactggt-attagtaagaaatatgaccttaaat--catttattaattttgtgactaccca------ctgtcatttatgtttctattatttaattttttgcttttt-cagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
 | || | |   | ||   || |      | ||||  ||| |   ||   | ||  | | ||      || |||  |       |||   ||   ||| ||    || |||||| |||| || || || ||||| |||||||||||||||||||| ||||||||||||||||||||||| ||  | || ||| | ||| | |||||||| |
gtgaccgattgctcgtctaaatttctttttgaaatttcatcttcgaaagatatgtttgctcaaaatatctatcaagtgaacgcttatcggttggctttgtgtgccttgcagAGCCTGAAACATAATCCGAATGGCAGGTTTGTGGTAGTTTGTGGTGATGGTGAGTATATTATCTACACAGCTCTTGCTTGGAGGAATCGATCATTTGGTT

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|164101548|gb|ES030195.1|ES030195
EST:     CCGTTAAAGAGCTAGGGACCTGCGATCTTTATCCTCAA                         AGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGT
genomic: CCGTTAAAGAGCTAGGGACCTGCGATCTTTATCCTCAAgtaagtggca ... gctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
                                 atttaat  putative branch site (score: 4)
                                       ttttttgctttttc  CT-rich tract
                tcatttatgtttctat  TA-rich tract