Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagacactggcctttggttagattaatgactaggatggtcgactctcactactttgttgcatatattcatgtgcttaccttgttttttttttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGCACAACAGTATTATCGTCTGTACAAG

Basic information

species Oryza sativa
transcript LOC_Os03g26970.1
intron # 4
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|27548112|gb|CA766216.2|CA766216
EST:     TCTGTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: TCTGTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|58673780|gb|CK062466.1|CK062466
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|33681297|gb|CF309536.1|CF309536
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|218490861|gb|FG966652.1|FG966652
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88313637|gb|CI671766.1|CI671766
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|569227|gb|D40076.1|D40076
EST:     GTNCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTNAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88580311|gb|CI697228.1|CI697228
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAA
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAA
EST: gi|88570436|gb|CI661809.1|CI661809
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAA
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAA
EST: gi|4880857|gb|AU065156.1|AU065156
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88342989|gb|CI641515.1|CI641515
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|33808224|gb|CF330001.1|CF330001
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAA-ATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88580702|gb|CI697646.1|CI697646
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTNTTAGTG
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTG
EST: gi|58669010|gb|CK057696.1|CK057696
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCC
EST: gi|58656409|gb|CK045089.1|CK045089
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88740256|gb|CI763764.1|CI763764
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACT
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACT
EST: gi|58597692|gb|CK008220.1|CK008220
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|218489822|gb|FG967489.1|FG967489
EST:     GTGCAAAAGATTTAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88827968|gb|CI778533.1|CI778533
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGC
EST: gi|55435846|gb|CV731059.1|CV731059
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|33662862|gb|CF293829.1|CF293829
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGG-TGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88406056|gb|CI593836.1|CI593836
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCG
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCG
EST: gi|40486330|gb|BX897911.1|BX897911
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|33691028|gb|CF319267.1|CF319267
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88351773|gb|CI617498.1|CI617498
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|58683283|gb|CK071970.1|CK071970
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88390466|gb|CI607502.1|CI607502
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88959392|gb|CI685873.1|CI685873
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTNTTAGTGAGGAAAAGTCGAAAGCAA
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAA
EST: gi|33654277|gb|CF276891.1|CF276891
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|33815449|gb|CF333578.1|CF333578
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|11233514|gb|AU164926.1|AU164926
EST:     GCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88574120|gb|CI665889.1|CI665889
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCA
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCA
EST: gi|33677213|gb|CF305452.1|CF305452
EST:     GTGCAAAAGATTCAGTCGTTGACTTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACT-CCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|88728844|gb|CI752354.1|CI752354
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGT
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGT
EST: gi|27576457|gb|CA999151.1|CA999151
EST:     GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTCGTCTACAG                         TGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
genomic: GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGC
EST: gi|8859749|gb|AU097067.1|AU097067
EST:     TGTTGGTCTACAG                         TGGCAT-GGGCCAAGACTNCCGTGTTTTTAGTG-GGNAAAAGTCGAANGC
genomic: TGTT-GTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCC-AGACTTCCGTG-TTTTAGTGAGG-AAAAGTCGAAAGC

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: 47 (upstream exon), 73 (downstream exon)
Score: 21

GTGCAAAAGATTCAGTCGTTGACTCCAAATATTGGTGTTGTCTACAGgtacttattt ... tttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGCACAACAGTATTATCGTCTGTACAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcactactttgttgcatatattcatgtgcttaccttgttttttttttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGCACAACAGTATTATCGTCTGTACAAG
                           tgcttac  putative branch site (score: 21)
                         tgtgcttaccttgttt  CT-rich tract
                                   ttgttttttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagacactggcctttggttagattaatgactaggatggtcgactctcactactttgttgcatatattcatgtgcttaccttgttttttttttcttccagTGGCATGGGGCCAGACTTCCGTGTTTTAGTGAGGAAAAGTCGAAAGCAAGCACAACAGTATTATCGTCTGTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attcatg