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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGATGACTTTCATGCTAAAGTGTCTGATTTTGGTTTGGCCAAACAGGCACCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggttgaccaccttgaagtactccccagatgtttctgctctgcttttgcttcatatagctgtcgtgctttcag

Basic information

species Oryza sativa
transcript LOC_Os01g14932.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14932.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G180065_T01 (Zea mays), 5'ss of exon 6
AGGATGACTTTCATGCTAAAGTGTCTGATTTTGGTTTGGCCAAACAGGCACCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggttgaccaccttgaagtactc------------cccagatgtttctgctctg------cttttgcttcatatagctgtcgtgctttcag
|| |||| || |||||||||||||| ||||||||| |||| |||||||| ||||||||| | || || ||||| || || |||||||||||||| ||||||||| | |  || ||   |  |  ||  |            |||||   ||| |  ||||      | ||  | |  ||   ||| | |  || |||
AGAATGATTTCCATGCTAAAGTGTCCGATTTTGGTCTGGCAAAACAGGCGCCGGAAGGTCGGACGAACTATCTTTCTACTCGTGTTATGGGAACTTTCGGgtaatctgaatgtccttttacatttagccatgggtccatggcccagcaatttattttctgaatttaccttcaccttgtacttctggcctttttgcag
















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|29625207|gb|CB630218.1|CB630218
EST:     CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGG                         GTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
EST: gi|88902229|gb|CI374837.1|CI374837
EST:     CCGGAAGGTTGCACAAATTATCTCTCAACACCTGTTATGGGAACATTCGG                         GTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
EST: gi|3763864|gb|AU030603.1|AU030603
EST:     CCGGAAG-TTGCACAAATTATCTCTCAACACGTGTTATGGGA-CATTCGG                         GTATGTAGCACCAGAGTATGCCATGACAGGACACTTGCTTGTNAAA-GCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
EST: gi|29619813|gb|CB624825.1|CB624825
EST:     CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGG                         GTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
EST: gi|29628587|gb|CB633598.1|CB633598
EST:     CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGG                         GTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA
genomic: CCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGA

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: 65 (upstream exon), 70 (downstream exon)
Score: 13

AGGATGACTTTCATGCTAAAGTGTCTGATTTTGGTTTGGCCAAACAGGCACCGGAAGGTTGCACAAATTATCTCTCAACACGTGTTATGGGAACATTCGGgtaagcaggt ... gtgctttcagGTATGTAGCACCAGAGTATGCAATGACAGGACACTTGCTTGTAAAAAGCGATGTATATAGCTATGGAGTTGTTCTACTTGAACTACTTACTGGGAGGAGG




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