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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCCCAATGTGGTGTACAAGGGGAAGCTCGACGCGCAGCGTCGCATCGCTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTGgtatcctattgtcttcaccttaatccttttgcattgctaacgatgtgcgtttgcttggtgccaatggtagttgggtacgtggtggttattgtgggaatgg...

Basic information

species Oryza sativa
transcript LOC_Os04g58750.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 3
GGCGCCCAATGTGGTGTACAAGGGGAAGCTCGACGCGCAGCGTCGCATCGCTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTGgtatcctat-tgtcttcaccttaatccttttgcattgctaacgatgtgcgtttgcttggtgccaatggtagttgggtacgtggtggtt-attgtgggaatgg-----
||||||||||||||| ||||||||||||||||| || ||||| ||||| ||||| ||| | || ||||| ||||| ||||| |||||||| |||||| |||||||| |  || |||| | || |  ||         ||||   || || | || | ||||  | |||||||| ||| | |||| ||| | | |||| ||       
GGCGCCCAATGTGGTATACAAGGGGAAGCTCGATGCCCAGCGCCGCATTGCTGTCAAGCGCTTTAACCGCTCTGCCTGGCCCGACCCGCGCCAGTTCCTGgtatcccacctgccttctctttcacgctcc-------ctaattgtgcgcatctggtgggtgtaactggtagttcggttcctggttgtttactttgggcattatagat
















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|33794016|gb|CF322898.1|CF322898
EST:     CTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTG                         GAAGAAGCTAAATCAGTTGGACAACTTCGGAGCAAAAGGTTAGCAAATTTG
genomic: CTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTGgtatcctatt ... tatgcttcagGAAGAAGCTAAATCAGTTGGACAACTTCGGAGC-AAAGGTTAGC-AATTTG
EST: gi|33675914|gb|CF304153.1|CF304153
EST:     CTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTG                         GAAGAAGCTAAATCAGTTGGACAACTTCGGAGCAAAAGGTTAGCAAATTTG
genomic: CTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTGgtatcctatt ... tatgcttcagGAAGAAGCTAAATCAGTTGGACAACTTCGGAGC-AAAGGTTAGC-AATTTG
EST: gi|29624788|gb|CB629799.1|CB629799
EST:     CTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTG                         GAAGAAGCTAAATCAGTTGGACAACTCCGGAGCAAAAGGTTAGCAAATTTG
genomic: CTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTGgtatcctatt ... tatgcttcagGAAGAAGCTAAATCAGTTGGACAACTTCGGAGC-AAAGGTTAGC-AATTTG
EST: gi|58669011|gb|CK057697.1|CK057697
EST:     CTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTG                         GAAGAAGCTAAATCAGTTGGACAACTCCGGAGCAAAAGGTTAGCAAATTTG
genomic: CTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTGgtatcctatt ... tatgcttcagGAAGAAGCTAAATCAGTTGGACAACTTCGGAGCAAA-GGTTAGCAA-TTTG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGCCCAATGTGGTGTACAAGGGGAAGCTCGACGCGCAGCGTCGCATCGCTGTGAAGAGGTTCAACCGTTCTGCATGGCCTGACCCGCGGCAGTTCTTGgtatcctattgtcttcaccttaatccttttgcattgctaacgatgtgcgtttgcttggtgccaatggtagttgggtacgtggtggttattgtgggaatgg

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG