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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacattgttgtttactctatatttctgtttggtagctgctggaaatttataatcagaggctaggtttgataccttggtgccattgtggatttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGTTCTTGATGCCGCCACCGGGGTACACTACTCTGCGCTCCGTTTGGAAGAG

Basic information

species Oryza sativa
transcript LOC_Os11g16370.1
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|88696045|gb|CI739620.1|CI739620
EST:     GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|88576240|gb|CI670385.1|CI670385
EST:     GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|88301528|gb|CI597221.1|CI597221
EST:     GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|58665119|gb|CK053805.1|CK053805
EST:     GCGAGCAGCGGTGGCGCCGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|117233504|gb|CT842322.1|CT842322
EST:     GCGAGCAGCGGTGGCGCCGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|88331762|gb|CI640793.1|CI640793
EST:     GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|58684586|gb|CK073273.1|CK073273
EST:     GCGAGCAGCGGTGGCGCCG-CCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|58689975|gb|CK078662.1|CK078662
EST:     GCGAGCAGCGGTGGCGCCGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|88346696|gb|CI656723.1|CI656723
EST:     GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|58655184|gb|CK043864.1|CK043864
EST:     GCGAGCAGCGGTGGCGCCGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|88398002|gb|CI585505.1|CI585505
EST:     CGAGCAGCGGTGGCGCTGCCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: CGAGCAGCGGTGGCGCTG-CCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|58653267|gb|CK041947.1|CK041947
EST:     GCGAGCAGCGGTGGGGCCGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|88718580|gb|CI742090.1|CI742090
EST:     GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|88340276|gb|CI652625.1|CI652625
EST:     GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|58693385|gb|CK082072.1|CK082072
EST:     GCGAGCAGCGGTGGCGCCGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|88344812|gb|CI624463.1|CI624463
EST:     GCGAGAAGCGGTGGCGCTGCCCCCTGGTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATAAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|58662773|gb|CK051459.1|CK051459
EST:     GCGAGCAGCGGTGGCGCCGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|88696044|gb|CI739619.1|CI739619
EST:     GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAANTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
EST: gi|58666921|gb|CK055607.1|CK055607
EST:     GCGAGCAGCGGTGGCGCCGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCG                         GTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT
genomic: GCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGT

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: 45 (upstream exon), 57 (downstream exon)
Score: 4

GTCTCCTCCGCTCGCCCCGCCGCCTGCGCCGATCTCCGCCCATCCCGCGAGCGAGCAGCGGTGGCGCTGCCCCCTGCTGCTTCCTCGCCGCCCCCCGCCGgtgagcaaac ... tttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGTTCTTGATGCCGCCACCGGGGTACACTACTCTGCGCTCCGTTTGGAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttataatcagaggctaggtttgataccttggtgccattgtggatttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGTTCTTGATGCCGCCACCGGGGTACACTACTCTGCGCTCCGTTTGGAAGAG
                   gtttgat  putative branch site (score: 4)
                    tttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacattgttgtttactctatatttctgtttggtagctgctggaaatttataatcagaggctaggtttgataccttggtgccattgtggatttgtggtagGTTCTTGGATCAATATATGGGTTCAACTTCAAGGCCAGTTGATGATGAAGTTCTTGATGCCGCCACCGGGGTACACTACTCTGCGCTCCGTTTGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - -ttgttgt
- - - - - - - - - - - - -ctgtttg
- - - - - - - - - - - - - - - - - -gctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgcc