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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgctgaagcttacccagatatatgattgtctttacatttcttatgattttcaatgctccagattttctcaacttcattgtgtgtgtgccttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCAGAAATTGCACGGGTAGATGCAAGCTGCTCCACGTTCATTCTAGTACACT

Basic information

species Oryza sativa
transcript LOC_Os01g06600.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G862219_T03 (Zea mays), 3'ss of exon 4
------agtgctgaagcttacccagatatatgattgtctttacatttcttatgattttcaatgctccagattttctcaacttcattgtgtgtgtgccttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCAGAAATTGCACGGGTAGATGCAAGCTGCTCCACGTTCATTCTAGTACACT
      || | |||| | ||   || |   ||||  | | ||||| | |||||  ||| | |||||||   |||||||| ||   || | || || |||||| ||||| |||||||||||||||||||| || || || |||||| |||||||| |||||||||||||||||||||||||||| ||||| || || ||        
cggtggagggttgaatcatattaagtt---tgatattatgtacatat-ttatg--ttttagtgctccaatatttctcaagtttgatgcgggtctggcttactgcagGGTTATGGGTGCCCAGGACTTTCCATTACTGCCAGTGCTGTTACTATGTCAGAAATTGCACGGGTAGATGCAAGCTGTTCCACATTTATACTG-------

upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G862219_T04 (Zea mays), 3'ss of exon 4
------agtgctgaagcttacccagatatatgattgtctttacatttcttatgattttcaatgctccagattttctcaacttcattgtgtgtgtgccttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCAGAAATTGCACGGGTAGATGCAAGCTGCTCCACGTTCATTCTAGTACACT
      || | |||| | ||   || |   ||||  | | ||||| | |||||  ||| | |||||||   |||||||| ||   || | || || |||||| ||||| |||||||||||||||||||| || || || |||||| |||||||| |||||||||||||||||||||||||||| ||||| || || || || ||||
cggtggagggttgaatcatattaagtt---tgatattatgtacatat-ttatg--ttttagtgctccaatatttctcaagtttgatgcgggtctggcttactgcagGGTTATGGGTGCCCAGGACTTTCCATTACTGCCAGTGCTGTTACTATGTCAGAAATTGCACGGGTAGATGCAAGCTGTTCCACATTTATACTGGTGCACT

upper sequence: LOC_Os01g06600.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0105g00460.t01 (Vitis vinifera), 3'ss of exon 4
agtgctgaagcttacccagatatatgattgtctttacatttcttatgattttcaatgctccagattttctcaacttcattgtgtgtgtgccttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCAGAAATTGCACGGGTAGATGCAAGCTGCTCCACGTTCATTCTAGTACACT
           |     | | |    ||   ||||   |||  | || |  ||||   |   ||   |   |  || ||   |  || ||| |    ||||| |||||||||||||| |||||  | || ||||||||||||||||  |||||| || |  |||| ||||| ||||| || || |||||| | || || |
----------gtactttatacactccatgtcctttttcttttatctg-tggtcaaaattatggaacatggaagtttaatca-gcttgggccat----cagGGTTATGGGTGCCCAGGTCTTTCCGTTACTGCAAGTGCTATTACTACTGCAGAAGTTTCCAGGGTTGATGCGAGCTGTTCTACTTTCATTTTGGTCCATT

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|2312322|gb|C28477.1|C28477
EST:     ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG                         GGATATGGGTGCCCAGGACTTTCAATANCAGCAAGTGCTATTACTATGGCA
genomic: ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAGgtaacaattt ... cttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
EST: gi|29666427|gb|CB662702.1|CB662702
EST:     ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG                         GGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
genomic: ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAGgtaacaattt ... cttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
EST: gi|29666426|gb|CB662701.1|CB662701
EST:     ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG                         GGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
genomic: ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAGgtaacaattt ... cttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
EST: gi|29676104|gb|CB672379.1|CB672379
EST:     ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG                         GGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
genomic: ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAGgtaacaattt ... cttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
EST: gi|58666043|gb|CK054729.1|CK054729
EST:     ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG                         GGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
genomic: ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAGgtaacaattt ... cttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
EST: gi|11863268|gb|AU063379.2|AU063379
EST:     ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG                         GGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGGC
genomic: ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAGgtaacaattt ... cttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGG-C
EST: gi|29666428|gb|CB662703.1|CB662703
EST:     ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG                         GGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
genomic: ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAGgtaacaattt ... cttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
EST: gi|29678764|gb|CB675039.1|CB675039
EST:     ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG                         GGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
genomic: ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAGgtaacaattt ... cttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
EST: gi|33675069|gb|CF303308.1|CF303308
EST:     ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAG                         GGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA
genomic: ATGCCATTCCTAAACTTTCAAGCCTCGGTGTAGCTGGAGGCACAATAAAGgtaacaattt ... cttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattttcaatgctccagattttctcaacttcattgtgtgtgtgccttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCAGAAATTGCACGGGTAGATGCAAGCTGCTCCACGTTCATTCTAGTACACT
                                           gccttac  putative branch site (score: 3)
                                            ccttact  CT-rich tract
                agatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgctgaagcttacccagatatatgattgtctttacatttcttatgattttcaatgctccagattttctcaacttcattgtgtgtgtgccttactacagGGATATGGGTGCCCAGGACTTTCAATAACAGCAAGTGCTATTACTATGGCAGAAATTGCACGGGTAGATGCAAGCTGCTCCACGTTCATTCTAGTACACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT