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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattgcctagtgacatctgaaatcatatcaattcagttggttcttctaatgccagcgctccacgatggcattgatattttcacttataaggtgagcatgttttttctgtttctgtagGTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCAATTTAATCAAACACCCAAAGTTCATCACTGATACCAAGGCCGCTATTG

Basic information

species Zea mays
transcript GRMZM2G166035_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 2
gtatgtattgcctagtgacatctgaaatcatatcaattcagttggttcttctaatgccagcgctccacgatggcattgatattttcacttataaggtgagcatgttttttctgtttctgtagGTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCAATTTAATCAAACACCCAAAGTTCATCACTGATACCAAGGCCGCTATTG
    ||| ||   |||  ||   |||||  ||| ||||   |||| | ||   ||| |||        ||   | |||||    | ||||    |||              |||   | |||| || || ||||   |||| ||||| || || |||||||| ||||||||||||||||| || || ||||||||||||| ||||| |||| ||||||| |
----gtactgtacagttccacgagaaatattattaatt-gtttgggttttggtatgtcag--------gacatccttgatcaacttactt----ggt--------------tgtacatatagGCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G10740.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtattgcctagtgacatctgaaatcatatcaattcagttggttcttctaatgccagcgctc-cacgatggcattgatattttcacttataaggtgagca-tgtttttt-ctgtttctgtagGTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCAATTTAATCAAACACCCAAAGTTCATCACTGATACCAAGGCCGCTATTG
                      ||     | || || |  ||  |||||     |  |   |||   |   | | ||||| |||   |   |  |  | |  | ||||  || ||||||    ||| || || |||| |||||||||||||||||| ||||  ||||||||||| ||| | ||||  ||||||||||| ||| |||| |||||  | |||||  
----------------------tggtgcta-attaacttcgt--gttctcgctgtaacgtagcttatatcttagtattgacattagaaaacaagaaattaataatgttacttactgttttgccagGCCATGGTGGAGCCAGAGCAGCTGAGTACGTGAAGCGCCATCTTTTCAGTAATCTGATCACCCACCCAAAGTTTATCTCTGACACCAAATCAGCTATAA
















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|19350739|gb|BM895271.1|BM895271
EST:     GACGACGTTGACGGAGAGAAAGTTGGAATGTTTGGTGTGTATGATG                         G-CATGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCA
genomic: GACGACGTTGACGGAGAGAAAGTTGGAATGTTTGGTGTGTATGATGgtatgtattg ... gtttctgtagGTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCA
EST: gi|6826953|gb|AW330596.1|AW330596
EST:     TTGACGGAGAGAAAGTTGGAATGTTTGGTGTGTATGATG                         GTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCA
genomic: TTGACGGAGAGAAAGTTGGAATGTTTGGTGTGTATGATGgtatgtattg ... gtttctgtagGTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCA
EST: gi|31359010|gb|CD443367.1|CD443367
EST:     GATAGACGACGTTGACGGAGAGAAAGTTGGAATGTTTGGTGTGTATGATG                         GTCATGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCA
genomic: GATAGACGACGTTGACGGAGAGAAAGTTGGAATGTTTGGTGTGTATGATGgtatgtattg ... gtttctgtagGTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatggcattgatattttcacttataaggtgagcatgttttttctgtttctgtagGTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCAATTTAATCAAACACCCAAAGTTCATCACTGATACCAAGGCCGCTATTG
      cattgat  putative branch site (score: 4)
                                   tgttttttctgtttct  putative PPT
           atattttcacttataa  TA-rich tract