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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGCTCAATGGGCTTCCCTATTGTTGGTGAGACCTTCCAATTTTTCAGAACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattcaaatagttaataattaactttttttggaatcagtatgctatatatagttaaactttaggagaaagaacattgttgatatgaagacactattgctctaaatatgaacaacacacacaataaatctaagttcggtgtactgaactatcag

Basic information

species Oryza sativa
transcript LOC_Os11g18570.1
intron # 1
splice site 5'
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|88387150|gb|CI577936.1|CI577936
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88576269|gb|CI670414.1|CI670414
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88430543|gb|CI569566.1|CI569566
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCTGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88413343|gb|CI581358.1|CI581358
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88433765|gb|CI582087.1|CI582087
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88347017|gb|CI628687.1|CI628687
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCA
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCA
EST: gi|88720494|gb|CI743793.1|CI743793
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88338690|gb|CI644147.1|CI644147
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAACCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88387498|gb|CI583016.1|CI583016
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|29636216|gb|CB641225.1|CB641225
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTGTGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88351956|gb|CI625956.1|CI625956
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88288407|gb|CI661612.1|CI661612
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88330460|gb|CI633672.1|CI633672
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88392657|gb|CI625479.1|CI625479
EST:     ACAAGTCCATCACTAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88824950|gb|CI775515.1|CI775515
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88417586|gb|CI581609.1|CI581609
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|29677429|gb|CB673704.1|CB673704
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88339446|gb|CI635424.1|CI635424
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88392565|gb|CI625387.1|CI625387
EST:     ACAAGTC-ATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|9865635|gb|AU101385.1|AU101385
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88385602|gb|CI564262.1|CI564262
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|29644153|gb|CB649160.1|CB649160
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88389734|gb|CI588054.1|CI588054
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88341423|gb|CI635621.1|CI635621
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88312236|gb|CI582574.1|CI582574
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88400457|gb|CI593532.1|CI593532
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|88341424|gb|CI635622.1|CI635622
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
EST: gi|66916795|gb|CX103643.1|CX103643
EST:     ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAG                         GTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC
genomic: ACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATC

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: 57 (upstream exon), 73 (downstream exon)
Score: 35

CGGGCTCAATGGGCTTCCCTATTGTTGGTGAGACCTTCCAATTTTTCAGAACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattc ... gaactatcagGTATGGACCTATATTCAAAACTAACATAGGAGGCCAGCACGTGGTCATATCCCTTGATCCCGAGGTGAACCAGTTCATATTTCAACAAGAGGGGAAGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGGCTCAATGGGCTTCCCTATTGTTGGTGAGACCTTCCAATTTTTCAGAACAAGTCCATCAATAGACATGCCAATTTACTACAAGCGAAGACTGGAGAGgttaggattcaaatagttaataattaactttttttggaatcagtatgctatatatagttaaactttaggagaaagaacattgttgatatgaagacactattgctctaaatatgaacaacacacacaataaatctaagttcggtgtactgaactatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA