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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctgcaaaagttgatgttatacacagggtgcctttgcatagacataactgtcatggaacaaactagtcactgatgttattttcttttctttaatgtagGTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAACACAAGGGAAACTTAGTGCTCCACGGATATTGCGGATTCACAAA

Basic information

species Oryza sativa
transcript LOC_Os12g06810.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06810.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 14
------tttctgcaaaagttgatgttatacacagggtgcctttgcatagacataactgtcatggaacaaactagtcactgatgttattttcttttctttaatgtagGTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAACACAAGGGAAACTTAGTGCTCCACGGATATTGCGGATTCACAAA
      |  |  |     |  |  |   ||||||||||| ||    ||  |||  || ||||     |   |  |  |||||| |  |||  ||| | ||||| || || || || || || || ||||||||||| || |||||||| |||||||| |||||||| ||||||||||||||||||||||| |||||||| 
taatgatgccccctgctatataaatctgacacagggtgcttt---gtaaccattgctttcataagtta---ttttttctgatgcttattttctttatataatgcagATGCGGGTTTTATTTACACCCTGCTGAAGGCTCGCCTGCACCAAACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAG
















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|27554489|gb|CA998389.1|CA998389
EST:     GTGGACTGTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAA                         GTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC
genomic: GTGGACTGTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAAgtaattgctc ... tttaatgtagGTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC
EST: gi|29666969|gb|CB663244.1|CB663244
EST:     TGGATTGTGGACTGTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAA                         GTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC
genomic: TGGATTGTGGACTGTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAAgtaattgctc ... tttaatgtagGTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC
EST: gi|29683579|gb|CB679854.1|CB679854
EST:     GTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAA                         GTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC
genomic: GTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAAgtaattgctc ... tttaatgtagGTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC
EST: gi|58600096|gb|CK010624.1|CK010624
EST:     TGGATTGTGGACTGTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAA                         GTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC
genomic: TGGATTGTGGACTGTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAAgtaattgctc ... tttaatgtagGTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC
EST: gi|29670914|gb|CB667189.1|CB667189
EST:     CTGTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAA                         GTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC
genomic: CTGTGTTGAGCATAATCGATTTCCAAAAGAGAATACAAAgtaattgctc ... tttaatgtagGTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataactgtcatggaacaaactagtcactgatgttattttcttttctttaatgtagGTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAACACAAGGGAAACTTAGTGCTCCACGGATATTGCGGATTCACAAA
                              tgttattttcttttct  CT-rich tract
                             atgttattttcttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctgcaaaagttgatgttatacacagggtgcctttgcatagacataactgtcatggaacaaactagtcactgatgttattttcttttctttaatgtagGTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAACACAAGGGAAACTTAGTGCTCCACGGATATTGCGGATTCACAAA

tttctgc
- - - - - -gttgatg
- - - - - - - - - - - - - - - - -ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - - tgtcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaaa