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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcactcttaaatattgtagcggatcatttaaaatcttggtactcaaaggttgtggccattgtcaaaaaaattcagGTCAAGTATCTTTGATGCTAATGCTGGGATTGGATTAAGCAAGTCCTTCATGAAACTTGTCTCCTGGTATGACAACGAATGGGGTTACAG

Basic information

species Arabidopsis thaliana
transcript AT1G16300.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16300.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 12
gtatgtcactcttaa-atattgtagcggatcatttaaaatcttggtactcaaaggttgtggccattgtcaaa----aaaattcagGTCAAGTATCTTTGATGCTAATGCTGGGATTGGATTAAGCAAGTCCTTCATGAAACTTGTCTCCTGGTATGACAACGAATGGGGTTACAG
||| ||   |||  |  ||  |  |   ||  | |     ||    |   |  |||||     | || |         |  |||||||||| ||||||||||| || ||||| |||||| | |||   ||||||||||| ||||| || |||||||||||||| ||||| |||||
gtaagtacttctagatgtaccgatgtaaattgtgttgtg-ctcaaaagggagtggttgacataactgcccctttctgcatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATTGGACTGAGCTCTTCCTTCATGAAGCTTGTGTCATGGTATGACAACGAGTGGGGCTACAG

upper sequence: AT1G16300.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 12
-------------gtatgtcactcttaaatattgtagcggatcatttaaaatcttggtactcaaaggttgtggccattgtcaaaaaaattcagGTCAAGTATCTTTGATGCTAATGCTGGGATTGGATTAAGCAAGTCCTTCATGAAACTTGTCTCCTGGTATGACAACGAATGGGGTTACAG
                 |  || |     |||| | ||   | | ||  ||| | | |      |  |      ||||| |     |  |||||||||| ||||||||||| || ||||| |||||| | |||   ||||||||||| || || || |||||||||||||| ||||| |||||
gtgactattttgatccagcgacgcaaccttattttggcctgtgagttggaatgtagctg-----aaatcactatcattgcctttgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATTGGACTGAGCTCTTCCTTCATGAAGCTCGTGTCTTGGTATGACAACGAGTGGGGCTACAG

upper sequence: AT1G16300.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 12
gtatgtcact-cttaaatattgtagcggatc---atttaaaatcttggtactcaaaggttg-tggccattgtcaaaaaaat-tcagGTCAAGTATCTTTGATGCTAATGCTGGGATTGGATTAAGCAAGTCCTTCATGAAACTTGTCTCCTGGTATGACAACGAATGGGGTTACAG
    || ||| ||| |||   ||  || | |   ||||       |||      ||||| | ||  ||||| |      || |||||||||| ||||||||||| || ||||| || ||| | |||   || |||||||| ||||| || |||||||||||||| ||||| |||||
----gtgactacttcaatccagtgacgtaacctaattttgccctgtggggtgggaaggtagctgatcattgccttctgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG

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|19741929|gb|AU227282.1|AU227282
EST:     ACAGAAGAAGATGTCGTCTCTAATGATTTTCTTGGAGATTCAAG                         GTCAAGTATCTTTGATGCTAATGCTGGGATTGGATTAAGCAAGTCCTTCAT
genomic: ACAGAAGAAGATGTCGTCTCTAATGATTTTCTTGGAGATTCAAGgtatgtcact ... aaaaattcagGTCAAGTATCTTTGATGCTAATGCTGGGATTGGATTAAGCAAGTCCTTCAT
EST: gi|164233552|gb|ES101888.1|ES101888
EST:     CTTGGAGATTCAAG                         GTCAAGTATCTTTGATGCTAATGCTGGGGATTGGATTAAGCAAGTCCTTCA
genomic: CTTGGAGATTCAAGgtatgtcact ... aaaaattcagGTCAAGTATCTTTGATGCTAATGCT-GGGATTGGATTAAGCAAGTCCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatcatttaaaatcttggtactcaaaggttgtggccattgtcaaaaaaattcagGTCAAGTATCTTTGATGCTAATGCTGGGATTGGATTAAGCAAGTCCTTCATGAAACTTGTCTCCTGGTATGACAACGAATGGGGTTACAG
                                     attgtcaaaaaaatt  TA-rich tract