Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccattaattttatgtgcttatattgttgattatgcttccatgtttcattttatcgtgctgcatgtgctaattccttcgtttttttgcttgtggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA

Basic information

species Oryza sativa
transcript LOC_Os01g59990.1
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|38480261|gb|CF964350.1|CF964350
EST:     CCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: CCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88321645|gb|CI672786.1|CI672786
EST:     ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|58604519|gb|CK015047.1|CK015047
EST:     CGCCGCCG-CA-CACCGCAGCTGCGCCGCTTCAAG                         GCAGGACA-TGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: CGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88351281|gb|CI623503.1|CI623503
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|58591772|gb|CF990080.1|CF990080
EST:     CCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: CCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88576762|gb|CI673287.1|CI673287
EST:     GCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: GCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|163922730|gb|EG712201.1|EG712201
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|163929077|gb|EG713022.1|EG713022
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|55434318|gb|CV730280.1|CV730280
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88579651|gb|CI688661.1|CI688661
EST:     GCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: GCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88336434|gb|CI649021.1|CI649021
EST:     TCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: TCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88351707|gb|CI617432.1|CI617432
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88402814|gb|CI613262.1|CI613262
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88724029|gb|CI749288.1|CI749288
EST:     ACCCCCCGCCGTCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88330914|gb|CI638322.1|CI638322
EST:     ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|218481886|gb|FG948632.1|FG948632
EST:     CGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: CGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|86908394|gb|CI300774.1|CI300774
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88350195|gb|CI623133.1|CI623133
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|55439109|gb|CV732856.1|CV732856
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|55434794|gb|CV730521.1|CV730521
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88350259|gb|CI623197.1|CI623197
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|55433285|gb|CV729700.1|CV729700
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|117244000|gb|CT848387.1|CT848387
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|55431287|gb|CV728657.1|CV728657
EST:     CCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: CCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88328544|gb|CI676754.1|CI676754
EST:     GCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: GCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|163928807|gb|EG711919.1|EG711919
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88327884|gb|CI648283.1|CI648283
EST:     TCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: TCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|33806682|gb|CF329222.1|CF329222
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88743518|gb|CI767026.1|CI767026
EST:     ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88404907|gb|CI685341.1|CI685341
EST:     GCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: GCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88577347|gb|CI673923.1|CI673923
EST:     ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|33654059|gb|CF276673.1|CF276673
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88571646|gb|CI663019.1|CI663019
EST:     ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88327281|gb|CI645058.1|CI645058
EST:     TCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: TCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|33690835|gb|CF319074.1|CF319074
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|33690719|gb|CF318958.1|CF318958
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|55440029|gb|CV733325.1|CV733325
EST:     ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
EST: gi|88688905|gb|CI732481.1|CI732481
EST:     ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAG                         GCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
genomic: ACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA

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: 37 (upstream exon), 46 (downstream exon)
Score: 71

TTCCCTACTCCCACCCCCCGCCGCCGCCGCCACCACCGCAGCTGCGCCGCTTCAAGgtaaatctcc ... tggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttatcgtgctgcatgtgctaattccttcgtttttttgcttgtggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA
                   tgctaat  putative branch site (score: 71)
                         ttccttcgtttttttg  CT-rich tract
                                 ttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccattaattttatgtgcttatattgttgattatgcttccatgtttcattttatcgtgctgcatgtgctaattccttcgtttttttgcttgtggaatccagGCAGGACATTGTGAAAGTTTCCCAAGTCTGAAAAGATGGTTCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - tatgtgc
- - - - - - - - - - - ttgttga
- - - - - - - - - - - - - - - - tgcttcc
- - - - - - - - - - - - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgt