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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGATGCGGACTATCTTAGGTATCGTGGCATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgtatttatcacttatctttttctgggggttgcacaaatatgagccattatgcttatgtcctgttactgatacttgctatgtcaactatttatc...

Basic information

species Oryza sativa
transcript LOC_Os02g32660.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32660.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G032628_T01 (Zea mays), 5'ss of exon 19
GGTGATGCGGACTATCTTAGGTATCGTGGCATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgtatttatcacttatctttttctgggggttgcacaaatatgagccattatgcttatgtcctgttactgatacttgctatgtcaact----atttatc-
|||||||| |||||||||||||||| ||| |||| ||||||||| |  || |||||   ||| ||| |||||||||  ||||||| | ||| | ||||   |||   | ||   |||| |  | |   | |  || | ||| |  |||   |  ||||||  ||||||  |    |   ||| 
GGTGATGCAGACTATCTTAGGTATCATGGTATGCAAGAGTTTGATCAGGCAATGCAACATCTTGAGCAAAAATATGAAgtatgttct-ttttttactt--ttttgatttggttctgca-aggtttccacaaacat-catatttgttgtgcattctacttgtaatgtcattttaaaaaaaatca
















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|86597068|gb|CI272663.1|CI272663
EST:     GCGCGATGCAGTCTCTCGAGGAAAAATATGGG                         TTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
genomic: GCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgta ... gttatttcagTTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
EST: gi|88412500|gb|CI688850.1|CI688850
EST:     ATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGG                         TTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
genomic: ATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgta ... gttatttcagTTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
EST: gi|88851918|gb|CI679476.1|CI679476
EST:     ATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGG                         TTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
genomic: ATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgta ... gttatttcagTTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
EST: gi|88582727|gb|CI700155.1|CI700155
EST:     ATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGG                         TTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
genomic: ATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgta ... gttatttcagTTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
EST: gi|86479150|gb|CI121783.1|CI121783
EST:     GCATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGG                         TTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
genomic: GCATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgta ... gttatttcagTTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
EST: gi|88432744|gb|CI690588.1|CI690588
EST:     ATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGG                         TTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
genomic: ATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgta ... gttatttcagTTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
EST: gi|66947037|gb|AU311881.1|AU311881
EST:     GCATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGG                         TTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG
genomic: GCATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgta ... gttatttcagTTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAG

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: 74 (upstream exon), 75 (downstream exon)
Score: 684

GGTGATGCGGACTATCTTAGGTATCGTGGCATGCTAGAGTTTGACCGCGCGATGCAGTCTCTCGAGGAAAAATATGGGgtatgttgta ... gttatttcagTTCATGACATCAGACCACCAGTACATATCTCGAAAGCATGAAGAGGATAAGATGATTATATTTGAGAAGGGAGATCTGGTATTTGTGTTCAACTTCCATT




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