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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtacttccttttgtatttagatttagattgcattcattcatcgtttgctgatagatagttatttagagctagttttctaatcttactgattactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACTGTGGATAAAAGGATGCAAGGTTATCGTCCTCGACATTCCTCTGTTGTTT

Basic information

species Oryza sativa
transcript LOC_Os01g25880.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G102015_T01 (Zea mays), 3'ss of exon 3
-ggtacttccttttgtatttagatttagattgc--attcattcatcgttt-gctgatagata--gttatttagagctagttttctaatcttactgattactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACTGTGGATAAAAGGATGCAAGGTTATCGTCCTCGACATTCCTCTGTTGTTT
 |||| |    ||    | |   || || | ||  |  |||| || |||| | |  ||  ||   ||  | | ||    | || | || ||| |      || |||||| ||||| ||||||||||| |  || ||| | ||||||||   |||||| ||||| ||||||| |||||||||| |||| ||||| || |||||||||
tggtattcttattctgttattttttcagttagctgaaccatttatagttttgttagtatttaccattgctaacaggagttgtttttattttatt------ttccagTCTTCTGGCGCCACATATTTCTTGGGGCATAATGTGGGAGATGGCAAAACTATGGATGAAAGGATACAAGGTTATCATCCTGGACATCCCGCTGTTGTTT

upper sequence: LOC_Os01g25880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G043819_T03 (Zea mays), 3'ss of exon 1
--ggtacttccttttgtatttagatttagattgcattcattcatcgtttgctgatagatagttatttagagctagttttctaatcttactgattactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACTGTGGATAAAAGGATGCAAGGTTATCGTCCTCGACATTCCTCTGTTGTTT
  ||      | |||||  ||   | |  || |    ||||  | ||    | || | ||||  | || || |   ||  |||| ||| || | | ||||||||| ||||| ||||||||||| | | | ||  | |||||||||  |||||||||||| ||||| |||||||||||| |||| ||||| || ||| |||||
ttggctgaatcatttgttcttttttatcaatagttgacatttcttgtacagt-attggtagtagtgtacaggttcgttgataat-ttattggtcattttcagTCTTCTGGCACCACATATTTCTTATAGCATTGTCTGGGAGATAGCAAAACTGTGGATGAAAGGCTGCAAGGTTATCATCCTTGACATCCCGCTGCTGTTT
















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|33805659|gb|CF328708.1|CF328708
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
EST: gi|58694799|gb|CK083486.1|CK083486
EST:     AAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATATTTCATCTGGGATA-TTTGGGAGATACTAAAAGC
genomic: AAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAA-C
EST: gi|88314179|gb|CI602511.1|CI602511
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATATTTCATGTGGGATAT
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATAT
EST: gi|88301045|gb|CI592225.1|CI592225
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATAT
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATAT
EST: gi|88313188|gb|CI594818.1|CI594818
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATA
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATA
EST: gi|38473157|gb|CF957289.1|CF957289
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
EST: gi|88300648|gb|CI587452.1|CI587452
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAAACG                         TCTCCTGGCTC-ACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
EST: gi|58595486|gb|CK006014.1|CK006014
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
EST: gi|88387818|gb|CI587906.1|CI587906
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATATTTCATCTGG
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGG
EST: gi|88386515|gb|CI575293.1|CI575293
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGT-CTAACCCG                         TCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
EST: gi|33689062|gb|CF317301.1|CF317301
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACT
EST: gi|88312093|gb|CI580258.1|CI580258
EST:     TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCG                         TCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAA
genomic: TTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAA

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: 49 (upstream exon), 75 (downstream exon)
Score: 9

CTTTTGGAAATGATGTTCTGTTAGAAAATGGAGAAATTGACCGAGCTCGCTTAGGACAGATTGTCTTTTCTGACCCGGAAAAACGCCAAGTTCTAAACCGgtacatctcg ... ttactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACTGTGGATAAAAGGATGCAAGGTTATCGTCCTCGACATTCCTCTGTTGTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgatagatagttatttagagctagttttctaatcttactgattactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACTGTGGATAAAAGGATGCAAGGTTATCGTCCTCGACATTCCTCTGTTGTTT
                                       tactgat  putative branch site (score: 9)
                                             ttactttc  CT-rich tract
      atagatagttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtacttccttttgtatttagatttagattgcattcattcatcgtttgctgatagatagttatttagagctagttttctaatcttactgattactttcagTCTCCTGGCTCCACATATTTCATCTGGGATATTTTGGGAGATACTAAAACTGTGGATAAAAGGATGCAAGGTTATCGTCCTCGACATTCCTCTGTTGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - cttttgt
- - - - - - - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttactg