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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACACATTCTCAATGATTATTGCTTTTAATGGGTACGACGAGAGAAAGAGAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaactaggtttcaattttttatttgagctgagcatctcttatgacagacctgacaatgcttcaacagattaatgtattttcataatgttgtatgca...

Basic information

species Oryza sativa
transcript LOC_Os02g17280.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G102021_T01 (Zea mays), 5'ss of exon 6
CCACACATTCTCAATGATTATTGCTTTTAATGGGTACGACGAGAGAAAGAGAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaactaggtttcaattttttatttgagctgag-catc-----tcttatgacagacctgacaatgcttcaacagattaatgtattttcataatgttgtatgca
||| ||||||||||||||||||||||||||||  || |||||| |||||| |||||||||||| ||||| |||||  ||||| ||  |||| |||  ||||||||||| | |  | | | |||   ||| | |||  |||        | |||   || ||||   || |||||    || | |  |||   || | |||| |   
CCATACATTCTCAATGATTATTGCTTTTAATGCATATGACGAGGGAAAGAAAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaaccatgccttattgtttgtgttgggttgaaacataatgaacttgatgcttgagctgattttgtttcaat--tttcacgagtttctctatt-ttgttt---
















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|88268165|gb|CI377902.1|CI377902
EST:     GAAGTGATCAAGTATTTGTCCCACTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|86546412|gb|CI186618.1|CI186618
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88255900|gb|CI354724.1|CI354724
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88296751|gb|CI540103.1|CI540103
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88205852|gb|CI205701.1|CI205701
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88488734|gb|CI426005.1|CI426005
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTNNNNNNNCTGCGTAATTGGTACACCACTAT
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCT--GGGGGCTGCGTAATTGGTACACCACTAT
EST: gi|89187835|gb|CI009819.1|CI009819
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|86886214|gb|CI321250.1|CI321250
EST:     GAAATGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88273370|gb|CI393776.1|CI393776
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|396941389|gb|HO188598.1|HO188598
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA

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

CCACACATTCTCAATGATTATTGCTTTTAATGGGTACGACGAGAGAAAGAGAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTATGCGTCATGGGTGCAGTGACGTTGCAATACTGCTGGCAAATGGTATGGC




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