Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttcactgaactctaaacatcttactttactttatctgtacatgttccagtaacttgccatgttgcccattattatttgtctccgaattctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGATCGCCGAGTTCCTTCACCAGGCAGTGACCATCTGCTTGGATGTTCAGAA

Basic information

species Oryza sativa
transcript LOC_Os12g22030.2
intron # 3
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|16575081|gb|BI802377.1|BI802377
EST:     ATGTCACCTG-TG-TGTCCGCATTG                         GTACACCTGCCATGACATCAAGGG-TTTGTTAGAGGAGGACTTTGTACAGA
genomic: ATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|86521243|gb|CI161449.1|CI161449
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|86486835|gb|CI129468.1|CI129468
EST:     TGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|88993404|gb|CI257832.1|CI257832
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|88220283|gb|CI219843.1|CI219843
EST:     CCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: CCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|88976061|gb|CI024306.1|CI024306
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|88222686|gb|CI220827.1|CI220827
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|86412835|gb|CI067240.1|CI067240
EST:     GCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: GCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|86521226|gb|CI161432.1|CI161432
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|87027893|gb|CI276249.1|CI276249
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|86510331|gb|CI152964.1|CI152964
EST:     CCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: CCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|88731473|gb|CI755086.1|CI755086
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|58589560|gb|CF987868.1|CF987868
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|86520924|gb|CI161130.1|CI161130
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|29661231|gb|CB657506.1|CB657506
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAA
EST: gi|86887626|gb|CI294260.1|CI294260
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|88203576|gb|CI203425.1|CI203425
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|86490953|gb|CI133586.1|CI133586
EST:     TGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|86514112|gb|CI156745.1|CI156745
EST:     TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|86435459|gb|CI106692.1|CI106692
EST:     TGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: TGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
EST: gi|89174045|gb|CI041938.1|CI041938
EST:     GCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTG                         GTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA
genomic: GCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGA

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), 69 (downstream exon)
Score: 23

TTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAAATGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCATTGgtcagtatct ... ctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGATCGCCGAGTTCCTTCACCAGGCAGTGACCATCTGCTTGGATGTTCAGAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagtaacttgccatgttgcccattattatttgtctccgaattctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGATCGCCGAGTTCCTTCACCAGGCAGTGACCATCTGCTTGGATGTTCAGAA
   cagtaac  putative branch site (score: 23)
                        attattatttgtct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttcactgaactctaaacatcttactttactttatctgtacatgttccagtaacttgccatgttgcccattattatttgtctccgaattctggttccagGTACACCTGCCATGACATCAAGGGGTTTGGTAGAGGAGGACTTTGTACAGATCGCCGAGTTCCTTCACCAGGCAGTGACCATCTGCTTGGATGTTCAGAA

- ttcactg
- - - - - - - -aaacatc
- - - - - - - - - - - - - - - - - - - gtacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - -acttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgcc