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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctacattccttaattcaaccctcttcatatcgtaatcagtgacaaacattggaagtatactttacctcattttgtgttctttcagTGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAAGAACTTCCATGCCCTCACGAGGTTAGACGAAAATCGTGCCAAATGCCAG

Basic information

species Arabidopsis thaliana
transcript AT5G58330.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G58330.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 6
gtaagctacattccttaattcaaccctcttcatatcgtaatcagtgacaaacattggaagtatactttacctcattttgtgttctttcagTGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAAGAACTTCCATGCCCTCACGAGGTTAGACGAAAATCGTGCCAAATGCCAG
||| |  |  ||  |   ||     ||     | || | ||     || |  ||      |  | || |  |  ||||    | ||  ||||| ||||||||  | || |||||||||||||| || ||||| ||||| |||||  | |||||||| || |||||| | ||||| ||||||
gtatggaatttttttatgttt---tctaagtgtgtcattattttatactattatcatgtttgaa-ttaagttttttttaaacttttgtagTGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG

upper sequence: AT5G58330.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtaagc-tacattccttaattcaaccctcttcatatcgtaatcagtg-acaaacattggaagtatactttacctc--attttgtgttctttc------agTGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAAGAACTTCCATGCCCTCACGAGGTTAGACGAAAATCGTGCCAAATGCCAG
                                         || ||| |   |   |   |       | ||  |   ||  |  |||  ||  | || |   |     | |  |   ||| ||| | |||||      ||||| ||||| ||| | ||||||||||| ||||| |||||||||||||| |||||  | || |||||||| || ||| | || ||||| |||
gtaagaagcattgatttttctttcgttcattcttcttttgtgtgagcatgtgtgtgtgtgtgtgttttttttattgatgttcttggtgtgcagtcctttgtcctccctgtcatttatgattgtgtttcctttcctatgcagTGCATTGATATGTATGAAAAATGCTCCAAACATACCTGCAAAGAACTTTCATGCTTTGACTAGGTTAGATGAGAATAGAGCAAAATGTCAG
















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|116454058|gb|EG496650.1|EG496650
EST:     GCCTCTCCTAACGTCAAGGTTCTTGTAGTGGGAAACCCTTGCAACACCAA                         TGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAAGAACTTCCA
genomic: GCCTCTCCTAACGTCAAGGTTCTTGTAGTGGGAAACCCTTGCAACACCAAgtaagctaca ... gttctttcagTGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAAGAACTTCCA
EST: gi|125266776|gb|EL280861.1|EL280861
EST:     GCCTCTCCTAACGTCAAGGTTCTTGTAGTGGGAAACCCTTGCAACACCAA                         TGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAA
genomic: GCCTCTCCTAACGTCAAGGTTCTTGTAGTGGGAAACCCTTGCAACACCAAgtaagctaca ... gttctttcagTGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAA
EST: gi|164109961|gb|ES068451.1|ES068451
EST:     GGTTCTTGTAGTGGGAAACCCTTGCAACACCAA                         TGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAAGAACTTCCA
genomic: GGTTCTTGTAGTGGGAAACCCTTGCAACACCAAgtaagctaca ... gttctttcagTGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAAGAACTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtaatcagtgacaaacattggaagtatactttacctcattttgtgttctttcagTGCCTTGATTTGTCTTAAAAATGCTCCCAACATTCCTGCAAAGAACTTCCATGCCCTCACGAGGTTAGACGAAAATCGTGCCAAATGCCAG
                                       ttttgtgttctttc  CT-rich tract
                         tatacttta  TA-rich tract