Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcccaccctcgatcttggccgcttgcgcgcttccacgatctgagtatcctgtcgcgtactggggtcttaattaatttactagtgaccgtgctcatcttcttcttcttcctcctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGCCCGGGCGGAGTGGTTTCTTTCTTGCACGGGACGTGCTCGACGGAATGCC

Basic information

species Oryza sativa
transcript LOC_Os02g41550.1
intron # 1
splice site 3'
intron type U2

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|88350676|gb|CI617531.1|CI617531
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|29675695|gb|CB671970.1|CB671970
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88300087|gb|CI582321.1|CI582321
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|29682325|gb|CB678600.1|CB678600
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88732740|gb|CI755917.1|CI755917
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88417079|gb|CI573794.1|CI573794
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88740193|gb|CI763701.1|CI763701
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88310178|gb|CI657602.1|CI657602
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88354916|gb|CI615797.1|CI615797
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88369212|gb|CI577675.1|CI577675
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88311323|gb|CI570397.1|CI570397
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTC-TTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88362176|gb|CI608567.1|CI608567
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88430315|gb|CI567334.1|CI567334
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGGGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|29622509|gb|CB627520.1|CB627520
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGACCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88426477|gb|CI576719.1|CI576719
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88392864|gb|CI624095.1|CI624095
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88411980|gb|CI566709.1|CI566709
EST:     GGTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88403509|gb|CI575393.1|CI575393
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88324704|gb|CI621717.1|CI621717
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88368149|gb|CI575031.1|CI575031
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88333112|gb|CI640955.1|CI640955
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88290627|gb|CI667000.1|CI667000
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88306172|gb|CI636553.1|CI636553
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|29678609|gb|CB674884.1|CB674884
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|55828239|gb|AU069003.2|AU069003
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88740892|gb|CI763407.1|CI763407
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88373225|gb|CI614561.1|CI614561
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88303380|gb|CI669028.1|CI669028
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88404267|gb|CI575755.1|CI575755
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC
EST: gi|88421886|gb|CI609764.1|CI609764
EST:     GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTG                         GGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGT
genomic: GCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGC

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: 52 (upstream exon), 46 (downstream exon)
Score: 2

GGCTCCGCTACCGTACACGCCCCGGAGGAAGCCCAGGCCCCGCCCATGCTGCTGAGCTCGTGATCCTGCGCTCCTGGCCACAGGCTGCGATTCGGCGTTGgtgcgcccac ... ctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGCCCGGGCGGAGTGGTTTCTTTCTTGCACGGGACGTGCTCGACGGAATGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattaatttactagtgaccgtgctcatcttcttcttcttcctcctccttgcagGGGTTTCTGGTCCGAGGCGGCCATCAAGATCCGTGCTTCTTGTCCTTTGGCCCGGGCGGAGTGGTTTCTTTCTTGCACGGGACGTGCTCGACGGAATGCC
  aattaat  putative branch site (score: 2)
                   ccgtgctcatcttctt  putative PPT
     taatttacta  TA-rich tract