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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgttgaatagcattaggtactattgctgtaaactgtgcactttactggacagtcttttcatgtcattgaaactaaacattgtacctcatgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG

Basic information

species Oryza sativa
transcript LOC_Os06g21390.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g21390.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G395842_T02 (Zea mays), 3'ss of exon 4
-cttgttgaatagcattaggtactattgctgtaaactgtgcactttactggacagtcttttcatgtcattgaaactaaacattg--tacct-catgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG
  |||||     | | |  ||| ||||    |   | ||  |    |       | ||||||| ||||   | ||| |||  |   | ||| |||||||  ||||||||||||||||| || |||||||||||||| |||||||| |||||||||||||| |||||||||||||| ||||| |||| ||| ||
atttgttagtgtgaact--gtagtattaac-tgttcagtaaagcccatcattttgacttttca-gtcaacaacactgaacccttgttgcctgcatgttttgcagCATGCCTACAGAGATGGCCGCTTGGAAGAGGTAATACTGCGGCATCTTGATGCTGATGATGGAAGTACAGTAATTGCAAAAAGTATCAG
















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|29659494|gb|CB655769.1|CB655769
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|218493054|gb|FG951374.1|FG951374
EST:     TTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAAAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|58687235|gb|CK075922.1|CK075922
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAAAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|86493358|gb|CI135991.1|CI135991
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAACCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|86496021|gb|CI138654.1|CI138654
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|86492823|gb|CI135456.1|CI135456
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|86498369|gb|CI141002.1|CI141002
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|88227716|gb|CI227196.1|CI227196
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|33690378|gb|CF318617.1|CF318617
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|86505484|gb|CI148117.1|CI148117
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|86501658|gb|CI144291.1|CI144291
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|89181230|gb|CI045313.1|CI045313
EST:     AACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: AACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|86500831|gb|CI143464.1|CI143464
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
EST: gi|218488371|gb|FG949752.1|FG949752
EST:     TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAG                         CATGCCTACAAAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT
genomic: TCGATTTTGGAACTGGTACTTGTCCCTTTGGGTCAAGCTGTTTCTACAAGgtagaaagct ... tgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggacagtcttttcatgtcattgaaactaaacattgtacctcatgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG
                          aactaaa  putative branch site (score: 2)
                         aaactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgttgaatagcattaggtactattgctgtaaactgtgcactttactggacagtcttttcatgtcattgaaactaaacattgtacctcatgtttgacagCATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG