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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattgataacaaggttaacaactttggcaatgccatactggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCACGGAAGCGGATGAACTCCAATCGGTCATACCAAAATGCAAACCCACTGA

Basic information

species Oryza sativa
transcript LOC_Os05g34650.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 11
gtaagtattgataacaaggttaacaactttggcaatgccatactggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttg-gtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCACGGAAGCGGATGAACTCCAATCGGTCATACCAAAATGCAAACCCACTGA---
|||||  |||||        ||     ||||| |       |||| | ||| || || || || | | |||||  ||||   ||||||   || |||||||||||| ||||| ||||| || ||||| |||||||||||| |||||||||||||||| ||||||||||| ||||| |||||  |||   |||||||||   
gtaagcgttgattg------tattctatttggtaggattccactgct-aaagttcttcgcgttttcttatcctcgtcaaccatgttttttattaacagGCACATGTGTTACTGCATTTCATCAATGCCTCACATGCTAACCTGAATGCACGGAAGCGCATGAACTCCAACCGGTCGTACCAGTATG---ACCCACTGAACA
















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|33381296|gb|CF196639.1|CF196639
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCNNNGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAANGCN
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|33666778|gb|CF297745.1|CF297745
EST:     TGCTCAAGGACTAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|29645587|gb|CB650594.1|CB650594
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|117223389|gb|CT846265.1|CT846265
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|218496920|gb|FG952344.1|FG952344
EST:     TGCTCAAGGACCAAGCAAAGCCGGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|86910785|gb|CI294785.1|CI294785
EST:     TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|58593357|gb|CF991665.1|CF991665
EST:     TGCTCAAGGACCAAGCAAAGCCGGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|58675486|gb|CK064173.1|CK064173
EST:     TGCTCAAGGACCAAGCAAAGCCGGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
EST: gi|58600585|gb|CK011113.1|CK011113
EST:     TGCTCAAGGACCAAGCAAAGCCGGATGATATTCTCAAAGCCGCTTTCCAT                         GCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA
genomic: TGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCA

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: 72 (upstream exon), 71 (downstream exon)
Score: 34

TGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattg ... tggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCACGGAAGCGGATGAACTCCAATCGGTCATACCAAAATGCAAACCCACTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttggtttacagGCACATGTATTACTACATTTTATTAATGCATCACATGCTAACTTGAATGCACGGAAGCGGATGAACTCCAATCGGTCATACCAAAATGCAAACCCACTGA
                           tcctaat  putative branch site (score: 34)
      aaatttgttt  TA-rich tract