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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTATTGCACTTTTGAAGAAAGGCAAAATGGAGGACAATTTGCTGGAATTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgttatcatgattttttgctgaacagaagtagttaaatgatattctgagttctagtgtttcattatgctctcttcag

Basic information

species Oryza sativa
transcript LOC_Os11g21990.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g21990.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G012416_T04 (Zea mays), 5'ss of exon 5
ATCTTATTGCACTTTTGAAGAAAGGCAAAATGGAGGACAATTTGCTGGAATTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgttatcatgattttttgc----tgaac---agaagtagttaaatgatattctgagttctagtgtttcattatgctctcttcag----------------------------------------------------------------
|| | |||||||||||||||||||||||||||||||||||| || |||| || |||||||| || || ||| | || |||||||||||||| ||||||||||||| |  |  | |  ||||||      |||||   | ||    ||  ||   ||  |  |||  |||  | |||||||   |   |                                                                  
ATTTGATTGCACTTTTGAAGAAAGGCAAAATGGAGGACAATCTGTTGGACTTCTTCCCATCAGCTAAGAGATCTTCTGAGGCTTTATCTGAGCATTTCACgtaagattctcccttccttttttctattttgaaccataaaatgtcttgtattgaatctttggtttcagt--tccattatgtcttacacgtgtaactttgtaaagctatgaattttatctttttgctaatattcttatttgtgcatggtcctcag

upper sequence: LOC_Os11g21990.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G877316_T02 (Zea mays), 5'ss of exon 5
ATCTTATTGCACTTTTGAAGAAAGGCAAAATGGAGGACAATTTGCTGGAATTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaag---ttgttatcatgattttttgctgaacagaa-gta--gttaaatg-atattctgagttctagtgtttcattatgctctcttcag-----------------------------------------------------------
|| | ||||| |||||||||||||| ||||||||||||||| || |||| ||||| ||||| || || ||| |||| |||||||||||||| ||||||| |||||   ||  |  |    | |||||  | | |||| |||  ||| |||   |    | ||||| | | |  | | |||      |  |                                                           
ATTTGATTGCGCTTTTGAAGAAAGGAAAAATGGAGGACAATCTGTTGGACTTTTTTCCATCAGCTAAGAGATCCTCTGAGGCTTTATCTGAGCATTTCATgtaagatctttctccccccctattttgaagcatagaatgtactgttgaatctgtgggttcagttccattatgccttcatgtgtaactttgtaaagctatggattttatttatctttttgctaatattattatttgtgcatggctctcag
















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|27554576|gb|CA998476.1|CA998476
EST:     TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|313080715|gb|HO213512.1|HO213512
EST:     TTTTTCCCATCGGCAAAGAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGT
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGT
EST: gi|29681979|gb|CB678254.1|CB678254
EST:     TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|33795765|gb|CF323752.1|CF323752
EST:     GGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: GGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|38473334|gb|CF957466.1|CF957466
EST:     TTTTTCCCATCGGCAAAGAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|29665732|gb|CB662007.1|CB662007
EST:     TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|33692466|gb|CF320705.1|CF320705
EST:     TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|88577225|gb|CI673787.1|CI673787
EST:     TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|58664831|gb|CK053517.1|CK053517
EST:     AGAACCTCCGAGGCTTTATCTGAACA-TTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: AGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|88388384|gb|CI683155.1|CI683155
EST:     TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|44673376|gb|CR286810.1|CR286810
EST:     TTTTTCCCATCGGCAAAGAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|86900378|gb|CI296421.1|CI296421
EST:     TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
EST: gi|218493049|gb|FG951369.1|FG951369
EST:     TTTTTCCCATCGGCAAAGAGAACCTCCGAGGCTTTATCTGAACATTTCAC                         TAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA
genomic: TTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgtt ... ctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTATTGCACTTTTGAAGAAAGGCAAAATGGAGGACAATTTGCTGGAATTTTTCCCATCGGCAAAAAGAACCTCCGAGGCTTTATCTGAACATTTCACgtaagttgttatcatgattttttgctgaacagaagtagttaaatgatattctgagttctagtgtttcattatgctctcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC