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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCATAACATCTCATCCTTGTTAACATTTCAGGTATATGATGTTACTTCTTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatatattttctttcatttcataattaatgatgaaactgactgtcaacattattaaaccattgccatctcaatatcaaagctgacccctcctctccaatgcacgtag

Basic information

species Oryza sativa
transcript LOC_Os10g37420.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37420.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G074169_T04 (Zea mays), 5'ss of exon 3
GACCATAACATCTCATCCTTGTTAACATTTCAGGTATATGATGTTACTTCTTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatatattttctttcatttcataattaatgatgaaactgactgtcaacattattaaaccattgccatctcaatatcaaagctgacccctcctctccaatgcacgtag
                                 || |||||||| ||| |||||||||||||||| |||||||| ||||| || |||||||| ||||||||| ||  |||                             |  || |||       | |  ||  ||||   ||  ||||  | ||||| | || ||||  |||| |   ||
---------------------------------GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccatac----------------------------atcgattgt-------acttcacgtttgcagccttgatattga-gctgatctctactcttgaatgtaaccag
















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|88213809|gb|CI213658.1|CI213658
EST:     TTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88992876|gb|CI035838.1|CI035838
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|86532760|gb|CI172966.1|CI172966
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|86484803|gb|CI127436.1|CI127436
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         CCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88471915|gb|CI409186.1|CI409186
EST:     CCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: CCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88279226|gb|CI400226.1|CI400226
EST:     GCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: GCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|8404428|gb|AU091782.1|AU091782
EST:     ATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: ATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88524600|gb|CI453535.1|CI453535
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88535430|gb|CI464230.1|CI464230
EST:     TTTATGGATGAGCACCCTGGTGGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTATGGATGAGCACCCTGGT-GGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88543482|gb|CI473494.1|CI473494
EST:     AGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: AGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88528942|gb|CI457226.1|CI457226
EST:     GTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: GTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88506506|gb|CI434012.1|CI434012
EST:     CGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: CGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88543852|gb|CI473895.1|CI473895
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88237426|gb|CI237275.1|CI237275
EST:     ATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCTAAGACGCAACCCATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: ATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88548592|gb|CI476404.1|CI476404
EST:     CGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: CGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|89171272|gb|CI040549.1|CI040549
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCCATGATTTTGAAGACCTTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88531066|gb|CI459505.1|CI459505
EST:     CCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTT-AAGNACATTGGCCACAGTGAATCAGCA
genomic: CCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAG-ACATTGGCCACAGTGAATCAGCA
EST: gi|88539124|gb|CI468209.1|CI468209
EST:     CTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: CTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88550119|gb|CI480069.1|CI480069
EST:     TAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88516485|gb|CI444139.1|CI444139
EST:     GGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: GGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88524332|gb|CI452232.1|CI452232
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88530846|gb|CI459272.1|CI459272
EST:     TAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|86531953|gb|CI172159.1|CI172159
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|11565047|gb|AU165683.1|AU165683
EST:     AAGTGTTGCTANCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCNCAGTGAATCAGCAA
genomic: AAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|29628272|gb|CB633283.1|CB633283
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88474025|gb|CI411296.1|CI411296
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88556229|gb|CI486543.1|CI486543
EST:     AGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: AGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88553330|gb|CI483434.1|CI483434
EST:     ATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: ATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88481908|gb|CI419179.1|CI419179
EST:     ATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: ATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88530147|gb|CI458444.1|CI458444
EST:     CTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: CTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88539916|gb|CI469914.1|CI469914
EST:     GATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: GATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88908451|gb|CI091044.1|CI091044
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88481857|gb|CI419128.1|CI419128
EST:     GCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: GCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88546444|gb|CI476081.1|CI476081
EST:     TGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|88536769|gb|CI464555.1|CI464555
EST:     GCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: GCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
EST: gi|38474501|gb|CF958634.1|CF958634
EST:     TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG                         GCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA
genomic: TTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAA

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), 74 (downstream exon)
Score: 132

GACCATAACATCTCATCCTTGTTAACATTTCAGGTATATGATGTTACTTCTTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatata ... atgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAAGGGAGATGATGGAGAAGTATCTCATTGGGGAGATTGATGCTTCAACCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCATAACATCTCATCCTTGTTAACATTTCAGGTATATGATGTTACTTCTTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTGgtgagatatattttctttcatttcataattaatgatgaaactgactgtcaacattattaaaccattgccatctcaatatcaaagctgacccctcctctccaatgcacgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG