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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTAAACACGGATGGTCAATAAATGAATTTGGGGATTTGACAAGAGGTGCAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggtttaaggatccacatctgtcttttaccttccaaaagagtaagtagtaactagccctttaggatcaatcattggttatcctgatgttgctgcaat...

Basic information

species Oryza sativa
transcript LOC_Os04g48410.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g48410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G175728_T01 (Zea mays), 5'ss of exon 5
TGGTAAACACGGATGGTCAATAAATGAATTTGGGGATTTGACAAGAGGTGCAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggtttaaggatccacatctgtcttttaccttccaaaagagtaagtagtaact--agccctttaggatcaatcattggttatcctgatgttgct--gcaat
||||||||| ||||||||||||||| | ||||||||||||||||||||||||||||| |||||||| |||||||| ||  | ||| ||  |||  |||||||||  ||  |  |     |    ||     | |   | ||    || |   || |  ||    || |||| | |  |  ||| || |||| |   |  ||| |
TGGTAAACATGGATGGTCAATAAATCAGTTTGGGGATTTGACAAGAGGTGCAGAAAGCACTGGCAATGTCTATAATCCGCCAGATCATTTATCTGATAAGgtaatattccaacacttgaa---atcacggtcataaaataattacaaatgacaattggagaggcttgggatta-tgttatgttgtcttgatttcaattagcatt

upper sequence: LOC_Os04g48410.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv02s0025g04830.t01 (Vitis vinifera), 5'ss of exon 5
TGGTAAACACGGATGGTCAATAAATGAATTTGGGGATTTGACAAGAGGTGCAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggtttaaggatccacatctgtcttttaccttccaaaagagtaagtagtaactagccc---tttaggatcaatcattggttatc-ctgatgttgctgcaat
    ||||| || ||||| |||||||||||||| ||| | ||||||||||||| ||| ||||| ||||| |  || ||| |  |  |  || |  || |||     |     ||   |   || |  |  |  ||    | |  |    |||   || | |   |||      | |      |||   |   | |  |     |
---GAAACATGGGTGGTCTATAAATGAATTTGGTGATCTCACAAGAGGTGCAGCAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctgacttatgccttttatccaaattttttatgtttctacagtt-ttatctcaaatttgttgatagttgcaacttacaaccagtatctccttttt
















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|86602164|gb|CI260634.1|CI260634
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|86416602|gb|CI030613.1|CI030613
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|88443140|gb|CI546712.1|CI546712
EST:     TTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: TTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|88205774|gb|CI205623.1|CI205623
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|86860179|gb|CI322047.1|CI322047
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|38482288|gb|CF966333.1|CF966333
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|88452282|gb|CI555359.1|CI555359
EST:     CAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|89166005|gb|CI103095.1|CI103095
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|88506338|gb|CI433844.1|CI433844
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|86860224|gb|CI322078.1|CI322078
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGTGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|218484802|gb|FG943717.1|FG943717
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|29685204|gb|CB681479.1|CB681479
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|89163844|gb|CI100734.1|CI100734
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|88514871|gb|CI442525.1|CI442525
EST:     CCCATCGGATTATAGATCCCATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
EST: gi|88206894|gb|CI205210.1|CI205210
EST:     CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCTATAAG                         CCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA
genomic: CAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAA

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), 72 (downstream exon)
Score: 32

TGGTAAACACGGATGGTCAATAAATGAATTTGGGGATTTGACAAGAGGTGCAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggttta ... tctgaaacagCCTCTTGGTGACCTGGGAACACTAGAAGCTGGAGAGAAGGGTGAAGCCCAATTTTCAGCTTCAAAAGAGAAACTGAAAGTTGTTGACTTGATTGGCCGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTAAACACGGATGGTCAATAAATGAATTTGGGGATTTGACAAGAGGTGCAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggtttaaggatccacatctgtcttttaccttccaaaagagtaagtagtaactagccctttaggatcaatcattggttatcctgatgttgctgcaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG