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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtcttgccctgacatcgtgttttgaatcttcttttagctttttgaatttaaatatatgtaaagacacaatgtatcgctttgtctaaactctcttgcaacagGTCAAAAGCAAGGAAGGAACGAGTTTGTGATACGCTTGCAACCTTCAGAGGCAATGTACATGAAACTAACT

Basic information

species Arabidopsis thaliana
transcript AT5G40760.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 11
gtattgtcttgccctgacatcgtgttttgaatcttcttttagctttttgaat-ttaaatatatgtaaagacacaatgtatcgctttgtctaaactc-tcttgcaacagGTCAAAAGCAAGGAAGGAACGAGTTTGTGATACGCTTGCAACCTTCAGAGGCAATGTACATGAAACTAACT
  ||     | || |    || | ||||  |||    | |   |||||| || |||| |  ||||          | || |  ||   |||||| | || ||    |||| ||| ||||||||| || |||||||| |||||| | || || ||||| || |||||||||||||| |||
-aatgcagatacctttttttccttttttctatcagtatgttcttttttgtatcttaattgcatgtggg-------tctaacatttgaactaaacacatcctggtgaagGTAAAAGGCAAGGAAGAAATGAGTTTGTCATACGCCTTCAGCCATCAGAAGCCATGTACATGAAACTTACT

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G130230_T02 (Zea mays), 3'ss of exon 12
gtattgtcttgccctgacatcgtgttttgaatcttcttttagcttt-ttgaatttaaatatatgtaaagacacaatgtatc---gctttgtctaaac-tctcttgcaacagGTCAAAAGCAAGGAAGGAACGAGTTTGTGATACGCTTGCAACCTTCAGAGGCAATGTACATGAAACTAACT
             |  | ||  | | |||  |  |  | | ||| | ||   | | ||||    | |     |   ||||     ||   | ||||  |  | ||    |||  | ||||||||||| || |||||||| |||||| | ||||| ||||| || ||||||||||||||||||
-----------aacgaatattttatattggtttattatgttgctctgttatgtctgaataagaattagatatcctggtatttgaactaaatataaatataacctgatgaagGCAAGAAGCAAGGAAGAAATGAGTTTGTTATACGCCTCCAACCATCAGAAGCCATGTACATGAAACTAACT

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 12
gtattgtcttgccctgacatcgtgttttgaatcttcttttagctttttgaatttaaatatatgtaaagacacaatgtatcgctttgtctaaactctcttgcaacagGTCAAAAGCAAGGAAGGAACGAGTTTGTGATACGCTTGCAACCTTCAGAGGCAATGTACATGAAACTAACT
 |  |  ||  |    |        ||  || |  |   |  |  ||| || ||   |   || |  ||    | || |    |  |||   |||||||  |  |||  | || ||||| ||||| |||||||| |||||| |||| || ||||| || ||||||||||||||||| 
-tgattactaccttcaatgattctgttcaaagcaccagatttccatttaaacttgtctggttgcactga----acgtgtttaatcctctgtgctctctttta-tagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 12
gtattgtcttgccctgacatcgtgttttgaatcttcttttagctttttgaatttaaatatatgtaaagacaca-atgtatcgctttgtctaaactctcttgcaac-agGTCAAAAGCAAGGAAGGAACGAGTTTGTGATACGCTTGCAACCTTCAGAGGCAATGTACATGAAACTAACT
      | ||  |  ||     |||||    |  ||||   |     ||  | | ||| ||  ||   ||  |  | ||   |||  | ||||||   |       |||||||||||| || || || |||||||| |||||| ||||||||||||| || ||||||||||| || || 
------tattagctagagtgtatgtttcc--ttatcttgatggcaagtgcctattaatctaaatatcaacttatgtttaaaccttactgtaaacttattcctgtttagGTCAAAAGCAGGGGAGAAATGAGTTTGTTATACGCCTGCAACCTTCAGAAGCTATGTACATGAAGCTTACA

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|124798132|gb|EH887811.1|EH887811
EST:     CAAGGATGTCCCAGGCGACATATTCAGAT                         GTCAAAAGCAAGGAAGGAACGAGTTTGTGATACGCTTGCAA
genomic: CAAGGATGTCCCAGGCGACATATTCAGATgtattgtctt ... cttgcaacagGTCAAAAGCAAGGAAGGAACGAGTTTGTGATACGCTTGCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaatatatgtaaagacacaatgtatcgctttgtctaaactctcttgcaacagGTCAAAAGCAAGGAAGGAACGAGTTTGTGATACGCTTGCAACCTTCAGAGGCAATGTACATGAAACTAACT
                                  gtctaaa  putative branch site (score: 3)
                                         ctctcttgc  CT-rich tract
     atatatgtaaa  TA-rich tract