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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataccattatctaggataaaccatgtttttgtctttcacaatattgaaacgaaagtttgcttaaaagttcactgcttctcccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT

Basic information

species Oryza sativa
transcript LOC_Os01g04190.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 11
gta-taccattatctaggataaaccatgtttttgtctttcacaatattgaaacgaaagtttgcttaaaagttcactgcttctcccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT
||| | || || | |   | ||| ||||| ||| | ||       | | |    |  |   | | | |  ||||||  || || |  ||||||| ||| |||||| |||| ||| ||||||||||||| ||||| ||| ||||||||||||| ||   ||||||||||| |||||||||| |
gtaatgcccttgtgttcaacaaatcatgtgtttattttctctctcaatcagcaaatggagggttcata--ttcact-tttttctcccttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCACCTTATTCTGGTATTCTTGCTGTTGTTGGCACTGTTCT

upper sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G153704_T02 (Zea mays), 3'ss of exon 11
gta-taccattatctaggataaaccatgtttttgtctt---tcacaatattgaaacgaaag---tttgcttaaaagttcactgcttctcccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT
||| | || || | |   | ||| ||||| ||| | ||   || ||||    ||| |   |    ||  ||| |  ||| ||  || || |  ||||||| ||| |||||| |||| ||| ||||||||||||| ||||| ||| ||||||||||||| ||  |||||||||||| |||||||||| |
gtaatgcccttgtgttcaacaaatcatgtgtttattttctctctcaatcagcaaatgggggattcttctttacatattctct-tttttctcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCACCTTATTCTGGTACTCTTGCTGTTGTTGGCACTGTTCT
















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|38477850|gb|CF961983.1|CF961983
EST:     TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG                         GCTGCCTCAATGTTACTT
genomic: TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATGgtataccatt ... ccttttgaagGCTGCCTCAATGTTACTT
EST: gi|163921085|gb|EG710424.1|EG710424
EST:     TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG                         GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA
genomic: TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATGgtataccatt ... ccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA
EST: gi|38481055|gb|CF965144.1|CF965144
EST:     TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCAGG                         GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA
genomic: TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATGgtataccatt ... ccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA
EST: gi|7219969|gb|AU065196.2|AU065196
EST:     TGGACAAGCAANGAAGGAANAGCCTTCTGATAACAAGCTTTTCTGGCATG                         GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAANGGCTT-GGC
genomic: TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATGgtataccatt ... ccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAA-GGCTTTGGC
EST: gi|58598313|gb|CK008841.1|CK008841
EST:     TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG                         GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA
genomic: TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATGgtataccatt ... ccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA
EST: gi|27554385|gb|CA998285.1|CA998285
EST:     TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG                         GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA
genomic: TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATGgtataccatt ... ccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA
EST: gi|27576947|gb|CA999641.1|CA999641
EST:     TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG                         GCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA
genomic: TGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATGgtataccatt ... ccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacaatattgaaacgaaagtttgcttaaaagttcactgcttctcccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT
                                ttcactgcttctccct  CT-rich tract
     atattgaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataccattatctaggataaaccatgtttttgtctttcacaatattgaaacgaaagtttgcttaaaagttcactgcttctcccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT