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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacatttgccttatatatgctttaatactatacctttgttcttgcatttatttgcttatatattcgtccggcactttactgtagattttgacaagtaactcatgcattgaaagaagatatattaaggagagttgtaatcttttgatcacagttctgtctaactgcagTTACTTGAGTCAGCTTGGTGTCTTACCAACATTGCTGCTGGAAAACCTGAAGAAACAAAAGCTCTATTACCTGCATTGCCGTTACTCATTGCTCACCTTG

Basic information

species Arabidopsis thaliana
transcript AT5G03070.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g06470.1 (Oryza sativa), 3'ss of exon 3
gttacatttgccttatatatgctttaatactatacctttgttcttgcatttatttgcttatatattcgtccggcactttactgtagattttgacaagtaactcat-gcattgaaagaagatatattaaggagagttgtaatcttttgatcacagttct--gtctaactgcagTTACTTGAGTCAGCTTGGTGTCTTACCAACATTGCTGCTGGAAAACCTGAAGAAACAAAAGCTCTATTACCTGCATTGCCGTTACTCATTGCTCACCTTG
                       || ||   || |     |  |||  |  |      ||||| ||| |     | | ||  |  || ||  |   ||    |||   | |   | |   | | |||     ||||    |||| | |  ||  |||    | | | ||||||| || ||| |||||||||| ||||| ||||| || |||||  |||| |||||||||||| |  |  | |||||  | || || || |||||||||||||
----------------------gttgat--catgctgcactaattgtttcga---agctatatcttcattaaatattataaagctgagttgaatgtgttcagcattataattctatatcttttgttatttgaagtttgtctcttatcaggaccattcatgattttaatgcagTTGCTAGAGGCAGCTTGGTGCCTTACAAACATAGCAGCTGGGGAACCAGAAGAAACAAAATCCTTGCTGCCTGCTCTACCATTGCTTATTGCTCACCTTG

upper sequence: AT5G03070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G20090.1 (Glycine max), 3'ss of exon 3
-------gttacat-ttgccttatatatgctttaatactatacctttgttcttgcatttatttgcttatatattcgtccggcactttactgtagattttgac---aagtaactc---atgcattgaaagaagatatattaaggagagttgtaatcttttgatcacagttctgtctaactgcagTTACTTGAGTCAGCTTGGTGTCTTACCAACATTGCTGCTGGAAAACCTGAAGAAACAAAAGCTCTATTACCTGCATTGCCGTTACTCATTGCTCACCTTG
       ||| ||| || | ||  ||    || |||     || | | |   ||  | || |  |  |    ||   |  |||| |  ||||  ||  | |    |  |||      |    | |   ||||| || ||    |   ||  | | || || | |  ||  |      |||||||| |||||| ||||||||||||| || || |||||||| || || || ||||||||||||||| | || ||||||||||| || || |||||||| ||||
gtctgaagtttcatcttcctttgaatgatgttcaatg----acttgtatgaatgtttgtactctcaaaaggcttgagcaagcacatctctgtgcatccttatgcaagataatatggaaccagtagtgggaagaaattttcttaatgcttaca-ttttgtggtgaatgtctt------ctgcagTTGCTTGAGGCAGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAAGAAACAAAAGCTTTGTTGCCTGCATTGCCCTTGCTTATTGCTCATCTTG

upper sequence: AT5G03070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G05740.1 (Glycine max), 3'ss of exon 3
-------gttacat-ttgccttatatatgctttaatactatacctttgttcttgcatttatttgcttatatattcgtccggcactttactgtagat--tttgacaagtaactc---atgcattgaaagaagatatattaaggagagttgtaatcttttgatcacagttctgtctaactgcagTTACTTGAGTCAGCTTGGTGTCTTACCAACATTGCTGCTGGAAAACCTGAAGAAACAAAAGCTCTATTACCTGCATTGCCGTTACTCATTGCTCACCTTG
       ||| ||| || | ||  ||    || |||     || | | |   |   | |  |  |  |    ||   |  |||| |  ||||  ||  | ||  |  |||  |   |    | |   ||||| || ||    |   ||  | ||| | | | |  ||  |      |||||| | |||||| | ||||||||||| || || |||||||| || || || ||||||||| ||||||| || ||||||||||| || || |||||||| ||||
gtctgaagtttcatcttcctttgaatgatgttcaatg----acttctatgaatatttgtgctctcaaaacgcttgagcaagcacatctctgtgcatgctatgcaagataatacggaaccagtggtgggaagaaattttcttaatgcttacattctgt-ggtgaatgtctt------ctgcagGTGCTTGAGGCTGCTTGGTGTCTCACAAATATTGCTGCAGGGAATCCAGAAGAAACAGAAGCTCTGTTGCCTGCATTGCCCTTGCTTATTGCTCATCTTG

upper sequence: AT5G03070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g02290.t01 (Vitis vinifera), 3'ss of exon 3
gttacatttgccttatatatgctttaatactatacctttgttcttgcatttatttgcttatatattcgtccggcactttactgtagattttgacaagtaactcatgcattgaaagaagatatattaaggagagttgtaatcttttgatcacagttctgtctaactgcagTTACTTGAGTCAGCTTGGTGTCTTACCAACATTGCTGCTGGAAAACCTGAAGAAACAAAAGCTCTATTACCTGCATTGCCGTTACTCATTGCTCACCTTG
                                                     | | |||  | || |||   |  ||||      |  ||| || |  |     | | | |||||| |  |  | |  |   |   |||  | | || ||| |  |||   | ||||||| |||||| |||||||||| ||||| || ||||| ||||||||||| ||||||||||||||| |  | |||||||| ||  | || ||||||||  | |
-----------------------------------------------------tggattac-tgtttgtcttaccattta------aaattggcatggga-----gaactaaaagaaaactttctgattattatcacaat--tataattacaat--tgttatattgcagTTGCTTGAGGCAGCTTGGTGCCTTACAAATATTGCAGCTGGAAAACCAGAAGAAACAAAAGCTTTGGTGCCTGCATTACCACTGCTTATTGCTCATTTGG

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|19876777|gb|AU237608.1|AU237608
EST:     CAATACCTTTACTTGTGCAGTGTCTTTCATTTGGCTCCCCCGACGAACAG                         TTACTTGAGTCAGCTTGGTGTCTTACCAACATTGCTGCTGGAAAACCTGAA
genomic: CAATACCTTTACTTGTGCAGTGTCTTTCATTTGGCTCCCCCGACGAACAGgttacatttg ... ctaactgcagTTACTTGAGTCAGCTTGGTGTCTTACCAACATTGCTGCTGGAAAACCTGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagatatattaaggagagttgtaatcttttgatcacagttctgtctaactgcagTTACTTGAGTCAGCTTGGTGTCTTACCAACATTGCTGCTGGAAAACCTGAAGAAACAAAAGCTCTATTACCTGCATTGCCGTTACTCATTGCTCACCTTG
                                           gtctaac  putative branch site (score: 2)
                                       ttctgtct  CT-rich tract
     tatattaa  TA-rich tract