Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGAGGAGCAAAGCCTGTTGTCAATCAGGGGGGTAGTGGGATAATTACTGCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttgaacctcacatggcttttaaccctattatattctggttttgatttttacaaaaatatcttgaatag

Basic information

species Oryza sativa
transcript LOC_Os01g05800.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05800.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G110063_T01 (Zea mays), 5'ss of exon 10
------TGGGAGGAGCAAAGCCTGTTGTCAATCAGGGGGGTAGTGGGATAATTACTGCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttgaacctcacatgg----ctt----ttaaccctattatattctggttttgatttttacaaa-aatatcttgaatag
      |||||||||| |||||||| || | | |||||| |||  |||||||||| |||||||||||||||||  | | ||||||||||||      ||| ||||||||| ||||||| |||  | |    |||    |||| ||| || | |||||| | | ||| | ||| | ||| ||   || ||
GGAAAATGGGAGGAGCCAAGCCTGTAGTGAGTGAGGGGGATAGGAGGATAATTACAGCAGGACGAGCAAAACGCTCTAATGCTCAACCAGC------TGGAGAAAGgtgcctttgaacttcattttgaatgcttaaacttaaacctcttctgttctggatataattctcacacacaatctcacaaacag

upper sequence: LOC_Os01g05800.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G839422_T01 (Zea mays), 5'ss of exon 9
------TGGGAGGAGCAAAGCCTGTTGTCAATCAGGGGGGTAGTGGGATAATTACTGCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttgaacctcacatggct-tttaaccctattatattctggttttgatttttacaaa-aatatcttgaatag
      |||||||||| |||||||| || | | |||| |||||||| |||||||| |||||||||||||||||  | | ||||||||| |||      || || |||||| ||||||| |||  | | |  |||| ||| || | |  ||| | | ||||| ||| | ||| ||   |  ||
GGAAAATGGGAGGAGCGAAGCCTGTAGTGACTGAGGGAGGTAGTGGAATAATTACCGCAGGACGAGCAAAACGCTCTAATGCTCAACCTGCC------GGAGAGAGgtgcctttgaacttcattttgatgcttaaacctcttctgtcttggctataattttcacagacaatctcgcaagcag
















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|29615536|gb|CB620548.1|CB620548
EST:     GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCCACCTGGTGAAAG                         ATTTAAGCAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT
genomic: GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttga ... tcttgaatagATTTAAACAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT
EST: gi|4714906|gb|AU056023.1|AU056023
EST:     GTACGAGTGCTCAACCAGCCCAACCTGGTGAAAG                         ATTTAAACAGCTGAAAGNAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT
genomic: GTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttga ... tcttgaatagATTTAAACAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT
EST: gi|66920591|gb|CX107439.1|CX107439
EST:     GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAG                         ATTTAAGCAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT
genomic: GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttga ... tcttgaatagATTTAAACAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT
EST: gi|14713818|gb|AU197781.1|AU197781
EST:     GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAG                         ATTTAAACAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT
genomic: GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttga ... tcttgaatagATTTAAACAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT
EST: gi|38482468|gb|CF966504.1|CF966504
EST:     GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAG                         ATTTAAGCAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGG
genomic: GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttga ... tcttgaatagATTTAAACAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGG
EST: gi|29620328|gb|CB625340.1|CB625340
EST:     GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAG                         ATTTAAGCAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT
genomic: GCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttga ... tcttgaatagATTTAAACAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 75 (downstream exon)
Score: 91

TGGGAGGAGCAAAGCCTGTTGTCAATCAGGGGGGTAGTGGGATAATTACTGCAGGACGAGCAAAACGTACGAGTGCTCAACCAGCCCAACCTGGTGAAAGgtgcttttga ... tcttgaatagATTTAAACAGCTGAAAGAAGAGGAGAGCAAGAGAAAAGGCAACAAAGCGCTTGCTGCAGGAGATTCAGATCTTTCAGCCTCAACATCAGAGGATGAAGAG




<











<


<