Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaggcactgataccattttattcatgaaccctgtgctcaactgtccaacaccttagaacctgacaatagttatacttgtgttatattctgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGCAGTCGGTGTTGTGGTGGGCTTCACATTGAAGAGAAGACTACGCCGGTGG

Basic information

species Oryza sativa
transcript LOC_Os01g05140.1
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|86533752|gb|CI173958.1|CI173958
EST:     TCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTCC
genomic: TCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88477348|gb|CI414619.1|CI414619
EST:     CACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCCCCGTCAGCTTTGC
genomic: CACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88206992|gb|CI206841.1|CI206841
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88203638|gb|CI203487.1|CI203487
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88555512|gb|CI485776.1|CI485776
EST:     GCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGNCCGCAGT                         TCGTGTTTTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|87019340|gb|CI279850.1|CI279850
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88210933|gb|CI209209.1|CI209209
EST:     GCCGCTTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88997988|gb|CI037873.1|CI037873
EST:     GCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88208440|gb|CI208289.1|CI208289
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|87025911|gb|CI282488.1|CI282488
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88210995|gb|CI212635.1|CI212635
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|87028309|gb|CI263651.1|CI263651
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|86534262|gb|CI174468.1|CI174468
EST:     CCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: CCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88506049|gb|CI433555.1|CI433555
EST:     CCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: CCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCA-GGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88212398|gb|CI212038.1|CI212038
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88239888|gb|CI239050.1|CI239050
EST:     TCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|86826897|gb|CI268789.1|CI268789
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|24208688|gb|AU225715.1|AU225715
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|86530303|gb|CI170509.1|CI170509
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88207501|gb|CI207350.1|CI207350
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|87020713|gb|CI267434.1|CI267434
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88211655|gb|CI211295.1|CI211295
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|86433286|gb|CI093629.1|CI093629
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|87007473|gb|CI280937.1|CI280937
EST:     CGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCCNAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTG
genomic: CGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCG-C-AGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTG
EST: gi|86847109|gb|CI285185.1|CI285185
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88208708|gb|CI208557.1|CI208557
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|163929194|gb|EG711003.1|EG711003
EST:     GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGC
EST: gi|88491361|gb|CI428633.1|CI428633
EST:     GCCGCCTTCTCCGAGCAGGCGCAGCAGGTCCTCGTGCCCAGGGCCGCAGG                         TCGTGTTGTCTCTGTATCAACTTGTACGAAGATCAGCGCCGTCAG-TGTTG
genomic: GCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCT-TTG

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: 70 (upstream exon), 70 (downstream exon)
Score: 15

AGCTGCAGGCGGCGGCGCAGGACGCGGCGAACTCCTCGTCGCGCTCGGCGGCCGCCTTCTCCGAGCAGGCGCACCAGGTCCTCGTGCCCAGGGCCGCAGGgtatactctc ... tgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGCAGTCGGTGTTGTGGTGGGCTTCACATTGAAGAGAAGACTACGCCGGTGG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaacaccttagaacctgacaatagttatacttgtgttatattctgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGCAGTCGGTGTTGTGGTGGGCTTCACATTGAAGAGAAGACTACGCCGGTGG
              acctgac  putative branch site (score: 15)
                                     ttatattctgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaggcactgataccattttattcatgaaccctgtgctcaactgtccaacaccttagaacctgacaatagttatacttgtgttatattctgtattgcagTCGTGTTGTCTCTCTATCAACTTGTACGAAGATCAGCGCCGTCAGCTTTGCAGTCGGTGTTGTGGTGGGCTTCACATTGAAGAGAAGACTACGCCGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- caggcac
- - - - - - - - - - -attcatg
- - - - - - - - - - - - - - - -cctgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgtt