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'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGAAGCGAGAAGGTTCAAATAATTCAGCTAGCAGCTCTCCCGATAGTGACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttccatttattgatccaacctagaataataaacatttttttatacatagtattgttaatttatgacttatttggtgttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g13790.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13790.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G152319_T02 (Zea mays), 5'ss of exon 12
---TAGGAAGCGAGAAGGTTCAAATAATTCAGCTAGCAGCTCTCCCGATAGTGACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttc-catttattgatccaacctagaat---aataa----acatttttttatacatagtattgttaatttatgacttatttggtgttgcag
    ||||||| |||||| ||||| | |||   |||||||||||| |||| ||||| ||| |||||||||||||| |||||||| |||| | ||||||||||||| || |  ||| | |||      |||||||    |||||    | |  |||   |   |    ||||| |||||||  ||||||  |||   ||
CTCCAGGAAGCAAGAAGGGTCAAACACTTC---TAGCAGCTCTCCTGATACTGACAATGAAGTTCATCCTTCAAATTCAGAAGGATTTCGAGGTTTTCTTCAGgtctgctgacatcttttgtgttctcctagaaccaaaataagtttatacgtttgagttgttgaccttgtttatttatgtattatttaatgtattag
















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|88728664|gb|CI752174.1|CI752174
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|29617185|gb|CB622197.1|CB622197
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|86592896|gb|CI270453.1|CI270453
EST:     CAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: CAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|29618832|gb|CB623844.1|CB623844
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|29621696|gb|CB626707.1|CB626707
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|15854139|gb|BI806935.1|BI806935
EST:     CATCCTTC-AACTCAGAAGGG-TTCAAT-TTTTCTTCAG                         GACTTAGCTGGA-CGGC-GTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: CATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|87022124|gb|CI259196.1|CI259196
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|29621640|gb|CB626651.1|CB626651
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|87014871|gb|CI271470.1|CI271470
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|86477380|gb|CI120013.1|CI120013
EST:     ACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGACCGCCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|29626961|gb|CB631972.1|CB631972
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|29626892|gb|CB631903.1|CB631903
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|29644351|gb|CB649358.1|CB649358
EST:     ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: ACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
EST: gi|86482080|gb|CI124713.1|CI124713
EST:     GTTTTCTTCAG                         GACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA
genomic: GTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAA

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: 67 (upstream exon), 52 (downstream exon)
Score: 34

TAGGAAGCGAGAAGGTTCAAATAATTCAGCTAGCAGCTCTCCCGATAGTGACAGTGATGTTCATCCTTCAAACTCAGAAGGGTTTCAATGTTTTCTTCAGgtttgttcca ... ggtgttgcagGACTTAGCTGGAGCGGCGGTTGCTCATAATCCTTGTATTGACGATGCCAAAGATGTAGAGTCACTTTGTGCTGAATCGCCACCTCGAAGTGACCACGATT




<











<


<