Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcaacgaatataattcattttctgtttcatgtgtattaatatcttgagttgacttaatactctttgttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT

Basic information

species Oryza sativa
transcript LOC_Os06g49110.1
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|29681115|gb|CB677390.1|CB677390
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29616370|gb|CB621382.1|CB621382
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29655802|gb|CB652077.1|CB652077
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29645008|gb|CB650015.1|CB650015
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29619108|gb|CB624120.1|CB624120
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29643724|gb|CB648731.1|CB648731
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29624058|gb|CB629069.1|CB629069
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29660427|gb|CB656702.1|CB656702
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29617546|gb|CB622558.1|CB622558
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29637541|gb|CB642550.1|CB642550
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29621569|gb|CB626580.1|CB626580
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29673911|gb|CB670186.1|CB670186
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29619411|gb|CB624423.1|CB624423
EST:     TTGGTGTTAACAGATTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29679002|gb|CB675277.1|CB675277
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29672090|gb|CB668365.1|CB668365
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|27577435|gb|CB000130.1|CB000130
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAACATTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29667711|gb|CB663986.1|CB663986
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29641133|gb|CB646140.1|CB646140
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29661434|gb|CB657709.1|CB657709
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29638674|gb|CB643683.1|CB643683
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29681299|gb|CB677574.1|CB677574
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29688150|gb|CB684425.1|CB684425
EST:     GTTTTGTGCTGTTTCC-CCTGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: GTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29687455|gb|CB683730.1|CB683730
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29682583|gb|CB678858.1|CB678858
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|27554454|gb|CA998354.1|CA998354
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29641824|gb|CB646831.1|CB646831
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29666981|gb|CB663256.1|CB663256
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29624056|gb|CB629067.1|CB629067
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29619315|gb|CB624327.1|CB624327
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|9788971|gb|BE530981.1|BE530981
EST:     GGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: GGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|58612032|gb|CK039744.1|CK039744
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTC
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTC
EST: gi|29615586|gb|CB620598.1|CB620598
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29624060|gb|CB629071.1|CB629071
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29688148|gb|CB684423.1|CB684423
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29637162|gb|CB642171.1|CB642171
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29660273|gb|CB656548.1|CB656548
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT

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), 56 (downstream exon)
Score: 65

GTCTACAAGTCTCGTGATGTTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtttcatgtgtattaatatcttgagttgacttaatactctttgttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACTATTCGCCTGCTCAAGGATAAATTCCCTGACATT
                                     tactctttgttccttc  CT-rich tract
        atgtgtattaatat  TA-rich tract