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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGATGGCCACGCAGACCCCTAACCAAAATAGCAGCATCCTTAAGAAACAGTTACCTGGTTGCTACACTACATTCAGTTACTATGCCTTCAAAAGCAGgtgcttacctcgttgtttcattattagcggctcgtttatgatcctaagcgttagtcaaaccacatcttctaatctgaagattatttgcagaaattcatttttctagatgatgaacatcttagtgtacttgtagaagttatttgacag

Basic information

species Oryza sativa
transcript LOC_Os05g40260.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g40260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G44940.1 (Glycine max), 5'ss of exon 4
-GTGGGATGGCCACGCAGACCCCTAACCAAAATAGCAGCATCCTTAAGAAACAGTTACCTGGTTGCTACACTACATTCAGTTACTATGCCTTCAAAAGCAGgtgcttacctcgttgtttcattattagcggctcgtttatgatcctaagcgttagtcaaaccacatcttctaatctgaagattatttgcagaaattcatttttctagatgatgaacatcttagtgtacttgtagaagttatttgacag
 || || ||||| || |||||  |  | ||| |||| ||  | || | ||| |||||  | || ||  ||||||||||  | |  | | |        |||||    |     |    || || |   |      |  || |        | | || ||      ||||   |||| |    ||| |    |||   ||||        ||||||||||||||||||||||  |||||||||| ||| 
GGTAGGGTGGCCGCGTAGACCGTTGTCAAAATTAGCTGCCGCTTTGAAAAATAGTTATATAGTAGCCTCACTACATTCTATAAGAAAGTCACATGGGTCAggtaaaaatagtatgacatctttctctcctctgtctaaattagttagttagctggttaagtgttttcttt--atcttattgctatct----aaacctattt--------gatgaacatcttagtgtacttggcgaagttatttaaca-

upper sequence: LOC_Os05g40260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G40890.1 (Glycine max), 5'ss of exon 5
GTGGGATGGCCACGCAGACCCCTAACCAAAATAGCAGCATCCTTAAGAAACAGTTACCTGGTTGCTACACTACATTCAGTTACTATGCCTTCAAAAGCAGgtgcttacctcgttgtttcattattagcggctcgtttatgatcctaagc-gttagtcaaaccacatcttctaatctgaagattatttgcagaaattcatttttctagatgatgaacatcttagtgtacttgtagaagttatttgacag
   || |||||||| |||||  |  | ||| |||| ||  | || | ||| || ||  | || ||  |||| |||||  | |  | | |  |     |||||          |    || |  |  |      || ||   |  | ||  |   || ||| |   |  | || ||| |    ||| |    |||   ||||        ||||||||||||||||||||||  |||||||||| ||||
---GGTTGGCCACGTAGACCATTGTCAAAATTAGCTGCCGCTTTGAAAAATAGCTATATAGTGGCCTCACTGCATTCTATAAGAAAGTCACCTGGGTCAGgtaaaagtagtatgacatcttgctgtgtcctctgtctaaattaattagttggctgttaaagctttttatttattcttatagctatct----aaacctattt--------gatgaacatcttagtgtacttggcgaagttatttaacag
















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|11026174|gb|AU162775.1|AU162775
EST:     CAGTTACCTGGTTGCTACACTACATTCAGTTACTATGCCTTCAAAAGCAG                         AGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAG-AACTTCAGACC
genomic: CAGTTACCTGGTTGCTACACTACATTCAGTTACTATGCCTTCAAAAGCAGgtgcttacct ... tatttgacagAGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACC
EST: gi|4716609|gb|AU057725.1|AU057725
EST:     TTACCTGGTTGGCTACACTTACATTCAGTTACTATGCCTTCAAAAGCCAG                         AGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGAC
genomic: TTACCTGGTT-GCTACAC-TACATTCAGTTACTATGCCTTCAAAAG-CAGgtgcttacct ... tatttgacagAGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGAC
EST: gi|89167805|gb|CI021504.1|CI021504
EST:     ACATTCAGTTACTATGCCTTCAAAAGCAG                         AGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACC
genomic: ACATTCAGTTACTATGCCTTCAAAAGCAGgtgcttacct ... tatttgacagAGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACC
EST: gi|88995783|gb|CI037135.1|CI037135
EST:     CAGTTACCTGGTTGCTACACTACATTCAGTTACTATGCCTTCAAAAGCAG                         AGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACC
genomic: CAGTTACCTGGTTGCTACACTACATTCAGTTACTATGCCTTCAAAAGCAGgtgcttacct ... tatttgacagAGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACC
EST: gi|89189069|gb|CI012219.1|CI012219
EST:     ATGCCTTCAAAAGCAG                         AGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCGGACC
genomic: ATGCCTTCAAAAGCAGgtgcttacct ... tatttgacagAGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACC

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: 50 (upstream exon), 34 (downstream exon)
Score: 6

GTGGGATGGCCACGCAGACCCCTAACCAAAATAGCAGCATCCTTAAGAAACAGTTACCTGGTTGCTACACTACATTCAGTTACTATGCCTTCAAAAGCAGgtgcttacct ... tatttgacagAGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACCATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCA




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