Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaatttcctttgcttgttttgcttgctgatatttttgtttggatggtgtttatatttattctgggcaaattgtcactttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACATCCTTCTTGGACTATGATCAAGAAAGCTTATGGACGCTCTCACATAAAAC

Basic information

species Oryza sativa
transcript LOC_Os01g45550.2
intron # 5
splice site 3'
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|86434306|gb|CI094649.1|CI094649
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|89179874|gb|CI044153.1|CI044153
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|89194724|gb|CI117161.1|CI117161
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|89164996|gb|CI102084.1|CI102084
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|88246655|gb|CI246504.1|CI246504
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|86477474|gb|CI120107.1|CI120107
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCCTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|86501615|gb|CI144248.1|CI144248
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|86592538|gb|CI253219.1|CI253219
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|86505347|gb|CI147980.1|CI147980
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|86494150|gb|CI136783.1|CI136783
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|86535239|gb|CI175445.1|CI175445
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|109712580|gb|CI105188.1|CI105188
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|87015309|gb|CI275499.1|CI275499
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|86521327|gb|CI161533.1|CI161533
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|89163486|gb|CI100376.1|CI100376
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|88225519|gb|CI225435.1|CI225435
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|89183756|gb|CI046321.1|CI046321
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|88514330|gb|CI441836.1|CI441836
EST:     CCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: CCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|87027442|gb|CI272207.1|CI272207
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|88222283|gb|CI222239.1|CI222239
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|86482461|gb|CI125094.1|CI125094
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|86486031|gb|CI128664.1|CI128664
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|89175799|gb|CI042820.1|CI042820
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|58675818|gb|CK064505.1|CK064505
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|88246381|gb|CI246230.1|CI246230
EST:     TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
EST: gi|87027635|gb|CI274199.1|CI274199
EST:     TTTGTTTTTGCAAAAGAATATAATGTCCACCCGGCCATCCTGAGCACAGC                         GGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT
genomic: TTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACAT

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: 67 (upstream exon), 50 (downstream exon)
Score: 6

GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGCgtaagcaatt ... ctttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACATCCTTCTTGGACTATGATCAAGAAAGCTTATGGACGCTCTCACATAAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttgtttggatggtgtttatatttattctgggcaaattgtcactttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACATCCTTCTTGGACTATGATCAAGAAAGCTTATGGACGCTCTCACATAAAAC
                                          tcacttttt  CT-rich tract
                tgtttatatttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaatttcctttgcttgttttgcttgctgatatttttgtttggatggtgtttatatttattctgggcaaattgtcactttttacagGGTAATTTTTGGCATGCTAATAGCTCTTCCAATCACATTGCTGTACTACATCCTTCTTGGACTATGATCAAGAAAGCTTATGGACGCTCTCACATAAAAC

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