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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaataaattctggttcttttcttttttcctctgcacctaaattaaatctgtgcacatatgacaaacactaaaattgattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g11614.1
intron # 5
splice site 3'
intron type U2

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|55408883|gb|CV721259.1|CV721259
EST:     AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG                         GAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
genomic: AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
EST: gi|86822847|gb|CI251887.1|CI251887
EST:     AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG                         GAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
genomic: AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
EST: gi|5004673|gb|AU069848.1|AU069848
EST:     AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG                         GAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
genomic: AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
EST: gi|89167327|gb|CI252858.1|CI252858
EST:     AAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG                         GAGCAACAGCTGCAAGATCTCAACTAAGACTTGAGGAAAAAG
genomic: AAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
EST: gi|8857332|gb|AU094650.1|AU094650
EST:     AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG                         GAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
genomic: AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
EST: gi|7378312|gb|AU088583.1|AU088583
EST:     AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG                         GAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
genomic: AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
EST: gi|86493995|gb|CI136628.1|CI136628
EST:     AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG                         GAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
genomic: AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
EST: gi|58602799|gb|CK013327.1|CK013327
EST:     AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG                         GACCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
genomic: AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
EST: gi|32948430|gb|BP185002.1|BP185002
EST:     AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG                         GAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
genomic: AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG

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: 75 (upstream exon), 62 (downstream exon)
Score: 446

AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAGgtactgaata ... gattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcacctaaattaaatctgtgcacatatgacaaacactaaaattgattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG
       taaattaaatctgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgaataaattctggttcttttcttttttcctctgcacctaaattaaatctgtgcacatatgacaaacactaaaattgattctgcagGAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA