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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaattacaattatatgtgatgcaatgcaagacctctagttttaatatgaattaaaattttgacatttttttttcatatgcag

Basic information

species Oryza sativa
transcript LOC_Os07g02350.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 7
GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatga-----------attacaattatatgtgatgcaa-tgcaagacctctagttttaatatgaattaaaattttgacatttttttttcatatgcag
||||||||||||||  | ||||||   || |||||||||||| | |||||||||||||| ||||||||||||||||||||||||||||  |           | || | || |  |||  ||   |      | | |    ||||||| ||  | ||| |||   ||||||      ||||||
GTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAGgtatagcacgccactgctcactagactttttggtggcgcgcctttgccgcatttttcattaatat-aaggagaatcttgt--ttttttggggggatgcag

upper sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 6
GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtata-tgaattacaatt--atatgtgatgcaatgcaagacctctagtt-ttaatatgaattaaaattttgacatttttttttcatatgcag---------
|||||||| |||||  | ||||||   || |||||||||||| | |||||||||||||| ||||| |||||||| ||||||||||| | |      |   |  | |     |   ||| |||| ||  | |  ||  | || |||  | ||      |||||||||    |             
GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatgccgctgctcaacagactttttgatggaagatctgcaatcatttttgtggattgcatttacactcttttttttttgcctttttgggatgcag
















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|58686212|gb|CK074899.1|CK074899
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|89194544|gb|CI116981.1|CI116981
EST:     AGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|29616864|gb|CB621876.1|CB621876
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|89194075|gb|CI116512.1|CI116512
EST:     CCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: CCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|94362908|gb|CI053069.1|CI053069
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|89174479|gb|CI110677.1|CI110677
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|88957426|gb|CI095367.1|CI095367
EST:     TGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: TGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|58679114|gb|CK067801.1|CK067801
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCGACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|89182336|gb|CI113705.1|CI113705
EST:     TTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: TTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|86491402|gb|CI134035.1|CI134035
EST:     CTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: CTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|58598121|gb|CK008649.1|CK008649
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|29657466|gb|CB653741.1|CB653741
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|2796293|gb|AA749587.1|AA749587
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTGGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|88993477|gb|CI110298.1|CI110298
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|86419015|gb|CI053816.1|CI053816
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|29662231|gb|CB658506.1|CB658506
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|27577759|gb|CB000454.1|CB000454
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|86418789|gb|CI053590.1|CI053590
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|89180390|gb|CI044669.1|CI044669
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|86259780|gb|CI065653.1|CI065653
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|86425532|gb|CI070629.1|CI070629
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|89169654|gb|CI110013.1|CI110013
EST:     GCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: GCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|29663347|gb|CB659622.1|CB659622
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|29661178|gb|CB657453.1|CB657453
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|29619982|gb|CB624994.1|CB624994
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|86490821|gb|CI133454.1|CI133454
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
EST: gi|86524746|gb|CI164952.1|CI164952
EST:     AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG                         GCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT
genomic: AACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCT

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), 73 (downstream exon)
Score: 23

GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaat ... tcatatgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCTAGTATCCCCAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtatatgaattacaattatatgtgatgcaatgcaagacctctagttttaatatgaattaaaattttgacatttttttttcatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG