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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcttaaacatttgcttactgcaagaaaatatgcattgattttcactgataatgtgcctttgttacacaaactggttaactgtatttggcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGACCGTGTGGGACCAAACCGTTGAGTATTGTGCATTCGCTTATCAGCAGTAT

Basic information

species Oryza sativa
transcript LOC_Os01g46510.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G824843_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------ttttcttaaacatttgc-----ttactgcaagaaaatatgcattgattttcactgataatgtgcctttgttacacaaactggttaactgtatttggcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGACCGTGTGGGACCAAACCGTTGAGTATTGTGCATTCGCTTATCAGCAGTAT
                                                                                      |  ||| |   |  ||      | |||         | | |  |||| |  || | |||  |  |||||| | || ||    |||    | ||    |  ||||||||||||||||| || |||||||| |||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||||
gtatatatttaagtatgttctttttacattttatgctagttcctgattcctgtagtgtctggatagttatttcttggctgatacattgctctgatgtacctgtaaagttcactttgcttccttgtactatgatctaaacagctaacat--ctttgtgagactaaa-aatta--cattttaaattggtgcagCTGGGAGACCTATCAGCCTGTTAGTGGCCTACTTGCACAACCTGAGTGGACTGTGTGGGACCAAACTGTTGAGTATTGTGCATTTGCTTATCAGCAGTAT

upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 13
ttttcttaaacatttgcttactgcaagaaaatatgcattgattttcactgataatgtgcctttgttacacaaactggttaactgtatttggcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGACCGTGTGGGACCAAACCGTTGAGTATTGTGCATTCGCTTATCAGCAGTAT
     | |||| | |  ||  ||  ||   | |   |    ||  ||    |  | |   ||||  |     |||  |||| | | ||||  |  | ||| |||||||| |  || |||||  | ||  ||||| | ||||| || ||||| |  |||||||||||||||||||| |||||||| || || ||||| || 
----gtgaaacttataatttttgtgagggtacaactacaagttcacaagttttctatagatttgacat---cactttttaattttgtttg--tgattcagTTGGGAGACATTTCAGCCTGTGGGGGGTTTACTTCCTCAGCCAGAATGGACTGCTTGGGACCAAACCGTTGAGTACTGTGCATTTGCATACCAGCAATAC
















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|58662672|gb|CK051358.1|CK051358
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAG                         CTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
EST: gi|58664662|gb|CK053348.1|CK053348
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAG                         CTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
EST: gi|58666107|gb|CK054793.1|CK054793
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAG                         CTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
EST: gi|58666827|gb|CK055513.1|CK055513
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAG                         CTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
EST: gi|58658218|gb|CK046898.1|CK046898
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAG                         CTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
EST: gi|58612809|gb|CK040521.1|CK040521
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAG                         CTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
EST: gi|86889062|gb|CI314678.1|CI314678
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAG                         CTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
EST: gi|25804329|gb|CA760290.1|CA760290
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAG                         CTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
EST: gi|58656516|gb|CK045196.1|CK045196
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAG                         CTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGAC
EST: gi|88399115|gb|CI603782.1|CI603782
EST:     GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAA-TTCCAGTTATACAG                         CTGGGAGACCTACCAACCCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGA
genomic: GATCCATTTTCCTCCAAAGAAGGGCCTCCTCAAAATTTCCAGTTATACAGgtattgatgt ... gcttctgcagCTGGGAGACCTACCAA-CCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgataatgtgcctttgttacacaaactggttaactgtatttggcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGACCGTGTGGGACCAAACCGTTGAGTATTGTGCATTCGCTTATCAGCAGTAT
                              ggttaac  putative branch site (score: 3)
                                              cttctgc  putative PPT
     ataatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcttaaacatttgcttactgcaagaaaatatgcattgattttcactgataatgtgcctttgttacacaaactggttaactgtatttggcttctgcagCTGGGAGACCTACCAACCTGTTAGCGGCCTACTTGCACAGCCTGAGTGGACCGTGTGGGACCAAACCGTTGAGTATTGTGCATTCGCTTATCAGCAGTAT

- - - - - catttgc
- - - - - - - - - tactgca
- - - - - - - - - - - - - - - - atgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaact