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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatcagacccaatcatgataagaaataattttgttttggagatgcacttcttgctggccacttatcttttttagatgcgtttgattggaatgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAACTCAACTAGCAAATTTCATGTCTGATCTCGACGTCCAGCTTCCATCAGCT

Basic information

species Oryza sativa
transcript LOC_Os01g58220.2
intron # 1
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|88348263|gb|CI638922.1|CI638922
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|325493936|gb|JG458460.1|JG458460
EST:     GCGTCGTCGTCTCCCTCGGCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATC
EST: gi|58588457|gb|CF986765.1|CF986765
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCGCTGCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|58586025|gb|CF984333.1|CF984333
EST:     GCGTCGTCGTCTCCCTCGCCTTTGCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|88407488|gb|CI586329.1|CI586329
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|33658937|gb|CF281550.1|CF281550
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|55415044|gb|CV727420.1|CV727420
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCATTT
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|58589437|gb|CF987745.1|CF987745
EST:     CGTCGTCGTCTCCCTCGCCTTTCCCCTCGCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACTAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: CGTCGTCGTCTCCCTCGCCTTTCCCCTC-CGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|38482489|gb|CF966524.1|CF966524
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCT-CGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|11026164|gb|AU162765.1|AU162765
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|33688622|gb|CF316861.1|CF316861
EST:     GCGTCGTCGTCTCCCTCGCCCTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|33691527|gb|CF319766.1|CF319766
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|33674678|gb|CF302917.1|CF302917
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|88744687|gb|CI768047.1|CI768047
EST:     TTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: TTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|88355852|gb|CI626293.1|CI626293
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|88396539|gb|CI601022.1|CI601022
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|25798364|gb|CA754325.1|CA754325
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|88344182|gb|CI654612.1|CI654612
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGNTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|58596881|gb|CK007409.1|CK007409
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|33656815|gb|CF279429.1|CF279429
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|38477626|gb|CF961759.1|CF961759
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCGTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGGTTTGAGACCAATCAAA
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCT-GTTTGAGACCAATCAAA
EST: gi|88733095|gb|CI756272.1|CI756272
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|33658878|gb|CF281491.1|CF281491
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|88725358|gb|CI748617.1|CI748617
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
EST: gi|9865752|gb|AU101502.1|AU101502
EST:     GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAG                         CTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC
genomic: GCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAAC

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: 64 (upstream exon), 61 (downstream exon)
Score: 141

GAAGCGCCCAGAACCAGAAGAGAGGTCTGCCCCGTGGTCAAGCCGTGCCGCGTCGTCGTCTCCCTCGCCTTTCCCCTCCGCTCCGCTTCGCCGATCAAGgtgaccttcc ... atgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAACTCAACTAGCAAATTTCATGTCTGATCTCGACGTCCAGCTTCCATCAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttcttgctggccacttatcttttttagatgcgtttgattggaatgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAACTCAACTAGCAAATTTCATGTCTGATCTCGACGTCCAGCTTCCATCAGCT
                                  gtttgat  putative branch site (score: 141)
                 ttatcttttttagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatcagacccaatcatgataagaaataattttgttttggagatgcacttcttgctggccacttatcttttttagatgcgtttgattggaatgtttgcagCTTGCATTGAGACAAAGAAATCAGCTTTCATCTGTTTGAGACCAATCAAACTCAACTAGCAAATTTCATGTCTGATCTCGACGTCCAGCTTCCATCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - -tcatgat
- - - - - - - - - - - gaaataa
- - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - -gatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - cttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgattg