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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTATTCCTTACGTCAATCTGAACCACTACGATCTCCCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgtacatgccaattcttttttttaatgttttcactcacttatctattggtattgcctttccgttttaggctaattatatggtgataaaacatat...

Basic information

species Oryza sativa
transcript LOC_Os03g49610.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49610.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AC217401.3_FGT002 (Zea mays), 5'ss of exon 5
GGCTTATTCCTTACGTCAATCTGAACCACTACGATCTCCCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgtacatgccaattcttttttttaatgttttcactcacttatctattggtattgcctttccgttttaggctaattatatggtgataaaacatat---
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GCCTTACTCCTTACGCCAACCTTAACCACTATGATCTTCCGCTTGCGCTTCAGAAGAAGTACCAAGGCTGGTTAGGCCCAAAAATTGTgtaag--ggagaaacagacttcttgtctttgttgcttcatgttgaaatatgtgaagagt-cttgtactatatgaacttgatacattctatacacacatagttg
















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|58658600|gb|CK047280.1|CK047280
EST:     TTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTGTGTTTCAAGACATATGGCGATCG
genomic: TTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58670861|gb|CK059547.1|CK059547
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         AGGTGTATTTTCGGACTATGCTGA
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGA
EST: gi|58673207|gb|CK061893.1|CK061893
EST:     TTGCCACCTTCCAGAAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: T-GC-AC-TTC-AGAAAAA-GTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58666291|gb|CK054977.1|CK054977
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58662636|gb|CK051322.1|CK051322
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         AGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58672509|gb|CK061195.1|CK061195
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58653737|gb|CK042417.1|CK042417
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|117229561|gb|CT859875.1|CT859875
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58671028|gb|CK059714.1|CK059714
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58663559|gb|CK052245.1|CK052245
EST:     CCACTTGCACTTCAGAAAAAGTATGCAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58664913|gb|CK053599.1|CK053599
EST:     CCACTTGCACTTCAGAAAACGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58678605|gb|CK067292.1|CK067292
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAGAAATTGT                         TGGTGTATTTGCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58654026|gb|CK042706.1|CK042706
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58678530|gb|CK067217.1|CK067217
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58670130|gb|CK058816.1|CK058816
EST:     CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTGGTTTCAAGACATATGGCGATCG
genomic: CCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCG
EST: gi|58612072|gb|CK039784.1|CK039784
EST:     CACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAGGTTGT                         TGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATC
genomic: CACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAA-ATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATC

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: 75 (upstream exon), 73 (downstream exon)
Score: 26

GGCTTATTCCTTACGTCAATCTGAACCACTACGATCTCCCACTTGCACTTCAGAAAAAGTATGAAGGCTGGTTAAGCCCAAAAATTGTgtaagtcgta ... ttttttgcagTGGTGTATTTTCGGACTATGCTGAGTTTTGTTTCAAGACATATGGCGATCGAGTCAAGAACTGGTTTACGTTTAATGAGCCAAGGATAGTAGCAGCACTT




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