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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcatatcatactgtgtagctatttatctttaaacatctgcatgtgttcaggactatcgccacatgagtagagctgagaagctgaccacattttcttgttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAAGGTAGAATTTGGCTTACCTGACCTGGAGGGCCGTACCCAAATATTCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g54340.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 8
gtattgcatatcatactgtgtagctatttatctttaaacatctgcatgtgttcaggacta--tcgccacatgagtagagctgagaagctgaccacattttcttgttttgtc-----agGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAAGGTAGAATTTGGCTTACCTGACCTGGAGGGCCGTACCCAAATATTCAAG
                | | |||   |  || | |  | |     |||  || |  | |   | |||| ||    ||  |  ||||||||||||| |||| || |||| ||     ||||||||||| || |||||||||||||| |||||||||||| ||||||| ||||||||||| ||  |||||||||||||||||||||||||||| || |||
---------------gtttataggc-tccatgtcttga-actgatatggctttaaaatttattggccatatcc-caggtcccagaagctgaccactttttgtttttttttccttccagGCCTGATACATTGGATCCTGCACTTCTGCGTCCTGGTCGTCTGGACAGAAAGGTAGAATTCGGGCTACCTGACCTGGAGGGCCGTACCCAAATCTTTAAG
















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|87006868|gb|CI285902.1|CI285902
EST:     GATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|29622230|gb|CB627241.1|CB627241
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|86846539|gb|CI280856.1|CI280856
EST:     GGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|58654487|gb|CK043167.1|CK043167
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|86427651|gb|CI072748.1|CI072748
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGTTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|66912920|gb|CX099768.1|CX099768
EST:     GGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|88218140|gb|CI217989.1|CI217989
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|86540292|gb|CI180498.1|CI180498
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|86848818|gb|CI295658.1|CI295658
EST:     TTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: TTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|58673769|gb|CK062455.1|CK062455
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|88982623|gb|CI028036.1|CI028036
EST:     TTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: TTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|88980874|gb|CI021004.1|CI021004
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|8857968|gb|AU095286.1|AU095286
EST:     GATGGGTTTGATGCGAAGGGAA-CATCAAGGTTCTGATGGCCACCAACAA                         GCCTGAAACCTTAGATC-TGCACTTCTACGTCCTGGTCGTTTG
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTG
EST: gi|86490075|gb|CI132708.1|CI132708
EST:     GGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|86427640|gb|CI072737.1|CI072737
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|88974022|gb|CI002684.1|CI002684
EST:     GATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|86540282|gb|CI180488.1|CI180488
EST:     GATGGGTTGGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTGTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|86415012|gb|CI069415.1|CI069415
EST:     CTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: CTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|86593357|gb|CI257997.1|CI257997
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|86526803|gb|CI167009.1|CI167009
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|25803583|gb|CA759544.1|CA759544
EST:     GATGGGTNTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTTTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
EST: gi|89194700|gb|CI117137.1|CI117137
EST:     GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAG                         GCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA
genomic: GATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAA

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), 71 (downstream exon)
Score: 43

GGGGTGATAATGAGGTTCAGCGTACCATGTTGGAAATTGTGAACCAACTCGATGGGTTTGATGCGAGGGGAAACATCAAGGTTCTGATGGCCACAAACAGgtattgcata ... gttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAAGGTAGAATTTGGCTTACCTGACCTGGAGGGCCGTACCCAAATATTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatcgccacatgagtagagctgagaagctgaccacattttcttgttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAAGGTAGAATTTGGCTTACCTGACCTGGAGGGCCGTACCCAAATATTCAAG
                           agctgac  putative branch site (score: 43)
                                      ttttcttgttttgtc  putative PPT
                                     attttctt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgcatatcatactgtgtagctatttatctttaaacatctgcatgtgttcaggactatcgccacatgagtagagctgagaagctgaccacattttcttgttttgtcagGCCTGATACCTTAGATCCTGCACTTCTACGTCCTGGTCGTTTGGACAGGAAGGTAGAATTTGGCTTACCTGACCTGGAGGGCCGTACCCAAATATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG