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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttactcagtactctagcttgattatattggttcctgtgaattttgttaggttataagaagtatttggtgagtgttcttgttggctttcttcagcttactggttggttttgttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT

Basic information

species Oryza sativa
transcript LOC_Os05g35140.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g35140.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G153358_T02 (Zea mays), 3'ss of exon 1
--gtgagtgttactcagtactctagcttgattatattggttcctgtgaattttgttaggttataagaagtatttggtgagtgttcttgttggctttcttcagcttactggttggttttgttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
  | ||||||| |        ||||||    |||||    ||   |  ||  |    | |  |  |     |||  |     ||  ||   || | | |  |  |  || ||  |||     ||||||| ||||||||||| |||||||||||| | ||||||||
gtgagagtgttgcagcagttcctagctcatatatatgtcctcactttgatgat----gatcttgtggttcttttaatctaacttgctgcgcgcgtgcgtgtgtgtg-tgttttttttctgggtttcagGAAATGTCATCGCTCTCTTCCTCTTCCTTTCCCCAGT
















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|88364482|gb|CI644560.1|CI644560
EST:     GCATCTATAACAGATGGAGGATTTGACAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|88336144|gb|CI647338.1|CI647338
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|88348551|gb|CI634146.1|CI634146
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|38473069|gb|CF957201.1|CF957201
EST:     CATCTATAACAGAATGGAGGATTTGGCGAAGTTCTTGTTTGGAGTTTCTG                         GGCAATGTCATCGCGCTCT
genomic: CATCTATAACAGA-TGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagG-CAATGTCATCGCGCTCT
EST: gi|88575402|gb|CI669547.1|CI669547
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCACT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|88573529|gb|CI665100.1|CI665100
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|33799249|gb|CF325482.1|CF325482
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|29662554|gb|CB658829.1|CB658829
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|88341534|gb|CI641286.1|CI641286
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|699864|gb|D46155.1|D46155
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTGCCTACTTT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGTGCCTACTTT
EST: gi|29629891|gb|CB634900.1|CB634900
EST:     GCATCTATAACAGATGGAGGATTTGGCGAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|88335261|gb|CI650226.1|CI650226
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|88338434|gb|CI645688.1|CI645688
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTNTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|86902517|gb|CI304336.1|CI304336
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
EST: gi|29657893|gb|CB654168.1|CB654168
EST:     GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTG                         GCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
genomic: GCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT

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), 37 (downstream exon)
Score: 119

TTTTAGTTTATCTGAAGGAGAGGGATTTGTAAGTGCAAGGAACTAAAGCGGCATCTATAACAGATGGAGGATTTGGCAAAGTTCTTGTTTGGAGTTTCTGgtgagtgtta ... gttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgagtgttcttgttggctttcttcagcttactggttggttttgttctttcagGCAATGTCATCGCGCTCTTCCTCTTCTTATCCCCAGT
                           agcttac  putative branch site (score: 119)
                                         ttttgttctttc  putative PPT
                                         ttttgtt  TA-rich tract