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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtctatgccaactgatcttttttctttttacatattttagcatctaccaatgtcttctttaaagtaggatacttgggctgatctgtctgattttctatttcagAACTTCAGCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTATCAGTGACTGTCTTTCTTGGCCGCTTTGACATGCGAATGATGCAG

Basic information

species Arabidopsis thaliana
transcript AT4G23000.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g04210.1 (Oryza sativa), 3'ss of exon 6
gtacgtctatgccaactgatcttttttctttttacatattttagcatctaccaatgtcttctttaaagtaggatacttgggctgatctgtctgattttctatttcagAACTTCAGCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTATCAGTGACTGTCTTTCTTGGCCGCTTTGACATGCGAATGATGCAG
||| |   ||| ||    | ||     |||  ||| |   || |  |  || | || ||             ||| | |    ||| ||  || | | |      || || ||| ||||||| |||||||| || ||||||||| | ||||| |||||| | ||  |||| || ||||||||||| |||||||||
gtatgctgatgacactctacct-----cttgctacctcgcttggtgtacac-agtgact-----------aaatattcg--tcgatttgcttgctctgc------agGACATCAACTGATTTATTTAAAACCGTTTTTGACCTCATGGTATCTGTGACTCTTTTCGTTGGTCGGTTTGACATGCGGATGATGCAG

upper sequence: AT4G23000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018356_T02 (Zea mays), 3'ss of exon 2
gtacgtctatgccaactgatcttttttctttttacatattttagcatctaccaatgtcttctttaaagtaggatacttgggctgatctgtctgattttctatttcagAACTTCAGCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTATCAGTGACTGTCTTTCTTGGCCGCTTTGACATGCGAATGATGCAG
                |||| ||  | |  |  ||   || |   | || | | |    |    |||||    |||   ||||| |       | ||| | || ||| || ||| ||||||| ||||||||||| ||||||||| |  |||| |||||| | ||| |||| || ||||||||||| |||||||||
-------------gtatgatattagt-caatacactagttcttata-ctgcaagtaatatggcaaaagttacttac--aggctggt-------aatttgttttgcagGACATCAACTGATTTATTTAAAACTGTCTTTGACCTCATGATATCTGTGACTCTGTTTGTTGGTCGATTTGACATGCGTATGATGCAG

upper sequence: AT4G23000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G36310.1 (Glycine max), 3'ss of exon 5
--gtacgtctatgccaactgatcttttttctttttacatattttagcatctaccaatgtcttctttaaagtaggatacttgggctgatctgtctgattttctatttcagAACTTCAGCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTATCAGTGACTGTCTTTCTTGGCCGCTTTGACATGCGAATGATGCAG
   |   |  ||   || |  | | ||| ||  ||   | ||  |   |      | |   | || || || |  |     |  || |    || | |   || | |||||| || |||||||| || ||||| || ||||||||||| |||||||||||||||||  |||| || ||||||||||| |||||||||
gtatgtatgcatataaaatattttgtttcctagtttttttttaaaattttatttcaaggggtgttgaaggttgtcttgaatgtgtggttacacttactaaataatgcagAACATCTGCTGATTTATTCAAAACAGTTTTTGACCTCCTGGTATCAGTGACTGTCTTCGTTGGGCGTTTTGACATGCGTATGATGCAG

upper sequence: AT4G23000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G08860.1 (Glycine max), 3'ss of exon 5
------gtacgtctatgccaactgatcttttttct--ttttacatattttagcatctaccaatgtcttctttaaagtaggatacttgggctgatctgtctgattttctatttcagAACTTCAGCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTATCAGTGACTGTCTTTCTTGGCCGCTTTGACATGCGAATGATGCAG
       |   | |||   || |  | | ||| |   ||||   | |||||   | |  ||| |  |  |  |   |    |   |  |  | |     ||  |   || | |||||| || |||||||| || ||||| || ||||||||||| |||||||||||||||||  |||| || ||||||||||| |||||||||
gtatgtatgtatgtatataaagtattttgtttcccagtttttttttttttaatttttttcaaggggtgttgaaggttgtcttgaatatgtggttacacttg-ctaaataatgcagAACATCTGCTGATTTATTCAAAACGGTTTTTGACCTCCTAGTATCAGTGACTGTCTTCGTTGGGCGTTTTGACATGCGTATGATGCAG

upper sequence: AT4G23000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 6
-------------gtacgtctatg--ccaactgatcttttttctttttacatatt------ttagcatctaccaatgtcttctttaaagtaggatacttgggctgatctgtctgat-tttctatttcagAACTTCAGCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTATCAGTGACTGTCTTTCTTGGCCGCTTTGACATGCGAATGATGCAG
              | ||||  |     |  |  || ||||| ||| |  | |        ||||     |  ||  |||   ||||     | ||  ||  || |  |  | |||  || | || |||||| ||||||||| | ||||| || |  ||||||||||| |||||||| ||||| ||| |||| |||||||||||||| |||||||||
gtatatgttcaatattcgtcatttatttagttattcctttttttttatgaagaggagggggttagttggaaagaaaatctcagttaa--ctagttaactgtcctcactttgccgatgcttgtgttgcagAACATCAGCTGATCTTTTTAAGACAGCTTTTGACCTCCTGGTATCAGTAACTGTGTTTGTTGGTCGCTTTGACATGCGCATGATGCAG

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|164207747|gb|ES121342.1|ES121342
EST:     AGACAACAAATGAAACCTAATTTCTTAGATATGGTTCCTTGGTATTCAGG                         AACTTCAGCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTAT
genomic: AGACAACAAATGAAACCTAATTTCTTAGATATGGTTCCTTGGTATTCAGGgtacgtctat ... tctatttcagAACTTCAGCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTAT
EST: gi|164130630|gb|ES149364.1|ES149364
EST:     AGACAACAAATGAAACCTAATTTCTTAGATATGGTTCCTTGGTATTCAGG                         AACTTCAGCCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTAT
genomic: AGACAACAAATGAAACCTAATTTCTTAGATATGGTTCCTTGGTATTCAGGgtacgtctat ... tctatttcagAACTTCAGC-TGATTTGTTTAAAACTGTGTTTGACCTCCTCGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtcttctttaaagtaggatacttgggctgatctgtctgattttctatttcagAACTTCAGCTGATTTGTTTAAAACTGTGTTTGACCTCCTCGTATCAGTGACTGTCTTTCTTGGCCGCTTTGACATGCGAATGATGCAG
                                    gtctgat  putative branch site (score: 4)
                                          ttttctatttc  CT-rich tract
                                         attttctattt  TA-rich tract