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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctctttggttcttgttttgtttttattttgagtaagatatgcattcatcagtgcaagtatatcagcgcttttgatttcatttttcttttttgatgcagGACGATCAATCTTTCTCTGAAAATGATGCCTTTTTTGCATGGACGTTCGAAAAACGGCATCCGCTATGGCAAACGCTTTTGTCCTTCTTCTGGCCTGTAT

Basic information

species Arabidopsis thaliana
transcript AT3G20920.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G07900.1 (Glycine max), 3'ss of exon 2
--ttctctttggttcttgttttgtttttattttgagtaagatatgcattcatcagtgcaagtatatcagcgcttttgatttcatttttcttttttgatgcagGACGATCAATCTTTCTCTGAAAATGATGCCTTTTTTGCATGGACGTTCGAAAAACGGCATCCGCTATGGCAAACGCTTTTGTCCTTCTTCTGGCCTGTAT---
  |          | |||| | ||||||  | ||    || | | | |   |  ||     | | |    |  | | |    ||||   | | ||    | | | || |||   || |||||||||||||| ||||||||||||||||| | |||||| ||||| || ||||| || ||  | || |||||||||||||| |   
gttaaaaccataatattgtatggttttttctctgcagcagtt-tacgtgagtaggtttctttctgtgtttgaatctaacaaaatttgattgtctt----cggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTCTGGCAGACACTCCTCTCATTCTTCTGGCCTGTGTTAA

upper sequence: AT3G20920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G45020.1 (Glycine max), 3'ss of exon 2
ttctctttggttcttgttttgtttttattttgagtaagatatgcattcatcagtgcaagtatatcagcgcttttgatttcatttttcttttttgatgcagGACGATCAATCTTTCTCTGAAAATGATGCCTTTTTTGCATGGACGTTCGAAAAACGGCATCCGCTATGGCAAACGCTTTTGTCCTTCTTCTGGCCTGTAT---
   | ||     | |  | |  | |  ||||   |    |     || | | |   | || | |    |  ||||| |  |    | |  ||   |   | | || |||   || |||||||||||||| ||||||||||||||||| | |||||| ||||| || ||||| || ||  | || || ||||||||||| |   
--atgttaaaaccatcatattgtatggttttttctcctctgc-tgtttacccgattaggtttctttctgtgtttgaatctaacaatttgattgtctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTTTGGCAGACACTCCTCTCGTTTTTCTGGCCTGTGTTAA

upper sequence: AT3G20920.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 2
ttctctttggttcttgttttgtttttattttgagtaagatatgcattcatcagtgcaagtatatcagcgcttt-tgatttcatttttcttttttgatgcagGACGATCAATCTTTCTCTGAAAATGATGCCTTTTTTGCATGGACGTTCGAAAAACGGCATCCGCTATGGCAAACGCTTTTGTCCTTCTTCTGGCCTGTAT---
   |   | ||||   || | ||   | |     |    ||  |||| |||   |  |   |||     |  | | | ||   ||      | || |  |  | ||||| |  || |||||||||||||||||||| |||||||| || |  ||||||   ||  | ||||| || ||| | || || ||||||||||| |   
---tgcattgttcaatttctcttggaaatcatgcttctgtaaccatttatccaggtcaagttattgataccatattactttgcttgctgactctgttttac-agGATCATTTATTTTCTGAAAATGATGCCTTTTTCGCATGGACATTTGTCAAACGGAGGCCATTGTGGCAGACACTTCTCTCATTTTTCTGGCCTGTGTTGA

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|164231860|gb|ES118412.1|ES118412
EST:     CCGGGAAGAAAAAGCTCTCTACTTGGCCTGCTCATTTGGAGATTTTCCGT                         GACGATCAATCTTTCTC
genomic: CCGGGAAGAAAAAGCTCTCTACTTGGCCTGCTCATTTGGAGATTTTCCGTgtaagttgat ... tttgatgcagGACGATCAATCTTTCTC
EST: gi|164132235|gb|ES058208.1|ES058208
EST:     CCGGGAAGAAAA-GCTCTCTACTTGGCCTGCTCATTTGGAGATTTTCCGT                         GACGATCAATCTTT
genomic: CCGGGAAGAAAAAGCTCTCTACTTGGCCTGCTCATTTGGAGATTTTCCGTgtaagttgat ... tttgatgcagGACGATCAATCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatcagtgcaagtatatcagcgcttttgatttcatttttcttttttgatgcagGACGATCAATCTTTCTCTGAAAATGATGCCTTTTTTGCATGGACGTTCGAAAAACGGCATCCGCTATGGCAAACGCTTTTGTCCTTCTTCTGGCCTGTAT
                                            ttttgat  putative branch site (score: 4)
                        cttttgatttcatttt  CT-rich tract
                         ttttgatttcattttt  TA-rich tract