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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaattttcatctctgtttttaaattttgttatgtaggtttggcatcgtcactgtgtgaatttaaccattttgctaaagcag

Basic information

species Oryza sativa
transcript LOC_Os05g06430.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06430.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G159369_T01 (Zea mays), 5'ss of exon 9
CTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt-----ttcatct---ctgtttttaaattttgttatgtaggtttggcatcgtcactgtgtgaatttaaccattttgctaaagcag---------------------------
|||||||||||||||| ||   ||| ||  |||| |||||||| |||| |||||| ||||| |||||||||||||| |||||||  ||  |||| ||||||||||   ||     |||  ||   || |  ||  |   |  |   | | |||  |||  | | | |||        ||||| |   |   ||                            
CTCTTGTGAAGGAGTTTCTCAATGCTGCTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAAgtactttcttccaccttcccctacactatgcttgcaagctactcgattgatttaacattcttattatgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccag

upper sequence: LOC_Os05g06430.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G008647_T02 (Zea mays), 5'ss of exon 6
CTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt-----ttcatct---ctgtttttaaattttgttatgtaggtttggcatcgtcactgtgtgaatttaaccattttgctaaagcag---------------------------
|||||||||||||||| ||   ||| |   |||| |||||||| |||| |||||| ||||| |||||||||||||| |||||||  ||  |||| ||||||||||   ||     |||  ||   || | |||  |   |  |   | | |||  |||  | | | |||        ||||| |   |   ||                            
CTCTTGTGAAGGAGTTTCTCAATGCTGTTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAAgtactttcttccaccttcccctacactatgtttccaagctactcgattgatttaacattcttattatgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccag

upper sequence: LOC_Os05g06430.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G404011_T01 (Zea mays), 5'ss of exon 7
CTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaattttcatctctgtttttaaattttgttatgtaggtt------tggcatcgtcactgtgtgaatttaaccattttgctaaagcag------------
||||||||| |||||| ||   ||| ||  |||| |||||||| |||| |||||| ||||| |||||||||||||| |||||||  ||  |||| ||||||||||   || |     ||     || | | |||| || | | |      | |  |   || | |   || || ||  |          |||            
CTCTTGTGATGGAGTTTCTCAATGCTGCTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAAgtact---ttcttccaccttcccctacactatgtt-tgcaagctactcgattgatttaacattctcaaaacttcactgtcaaatgtcgacaggtttaccatttg

upper sequence: LOC_Os05g06430.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G110742_T02 (Zea mays), 5'ss of exon 9
CTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt-----ttcatct---ctgtttttaaattttgttatgtaggtttggcatcgtcactgtgtgaatttaaccattttgctaaagcag---------------------------
|||||||||||||||| ||   ||| ||  |||| |||||||| |||| |||||| ||||| |||||||||||||| |||||||  ||   ||| ||||||||||   ||     |||  ||   || | |||  |   |  |   | | |||  |||  | | | |||        ||||| |   |   ||                            
CTCTTGTGAAGGAGTTTCTCAATGCTGCTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTTTGCAGCCAAgtactttcttccaccttcccctacactatgtttgcaagctacttgattgatttaacattcttattatgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccag

upper sequence: LOC_Os05g06430.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AC217311.3_FGT007 (Zea mays), 5'ss of exon 3
CTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt-----ttcatct---ctgtttttaaattttgttatgtaggtttggcatcgtcactgtgtgaatttaaccattttgctaaagcag---------------------------
|||||||||||||||| ||   ||| ||  |||| |||||||| |||| |||||| ||||| |||||||||||||| ||||||| |||  |||| ||||||||||   ||     |||  ||   || | |||  |   |  |   | | |||  |||  | | | |||        ||||| |   |   ||                            
CTCTTGTGAAGGAGTTTCTCAATGCTGCTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGTGGTTCTGCAGCCAAgtactttcttccaccttcccctacactatgtttgcaagctactcaattgatttaacattcttattatgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccag

upper sequence: LOC_Os05g06430.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G138616_T01 (Zea mays), 5'ss of exon 2
CTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt-----ttcatct---ctgtttttaaattttgttatgtaggtttggcatcgtcactgtgtgaatttaaccattttgctaaagcag---------------------------
|||||||||||||||| ||   ||  |   |||| |||||||| |||| |||||| ||||| |||||||||||||| ||||| |  ||  |||| ||||||||||   ||     |||  ||   || | |||  |   |  |   | | |||  |||  | | | |||        ||||| |   |   ||                            
CTCTTGTGAAGGAGTTTCTCAATGTTGTTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTGCTAAGCTTAGCGGTTCTGCAGCCAAgtactttcttccaccttcccctacactatgtttgcaagctactcgattgatttaacattcttattatgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccag

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|163925853|gb|EG714953.1|EG714953
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAACA                        
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCC-A-Agtactaaatt ... gctaaagca
EST: gi|163925853|gb|EG714953.1|EG714953
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAACA                        
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCC-A-Agtactaaatt ... gctaaagca
EST: gi|3768455|gb|AU032482.1|AU032482
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|58672427|gb|CK061113.1|CK061113
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|33803520|gb|CF327635.1|CF327635
EST:     GAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: GAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|58676547|gb|CK065234.1|CK065234
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGA
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGA
EST: gi|11026410|gb|AU163011.1|AU163011
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|86482186|gb|CI124819.1|CI124819
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|58690891|gb|CK079578.1|CK079578
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGA
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGA
EST: gi|86513133|gb|CI155766.1|CI155766
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAG                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|163927756|gb|EG710536.1|EG710536
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|87017864|gb|CI273886.1|CI273886
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         C
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcag-
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         C
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcag-
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         C
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcag-
EST: gi|5003011|gb|AU068120.1|AU068120
EST:     AATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: AATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|58683615|gb|CK072302.1|CK072302
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|33803570|gb|CF327660.1|CF327660
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|86593482|gb|CI264361.1|CI264361
EST:     CTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
genomic: CTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTC
EST: gi|58675064|gb|CK063751.1|CK063751
EST:     CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAA                         GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGA
genomic: CTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaatt ... gctaaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTGCGAAGCTCACTGGCCCTGCTGCCAAgtactaaattttcatctctgtttttaaattttgttatgtaggtttggcatcgtcactgtgtgaatttaaccattttgctaaagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC