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

...cacacatatacctctgcttgttttctaattaatctcaagagtgttgggctttgatatgggcctctcacaatctcgggctttgttaaaattaatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATCGACGAAGAGAAGGTGATGATGGAGTCGCTCATGTGCCTGAGGCGAGCCG

Basic information

species Oryza sativa
transcript LOC_Os06g49110.2
intron # 10
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|86870512|gb|CI320608.1|CI320608
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88971045|gb|CI387106.1|CI387106
EST:     TTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88961091|gb|CI096494.1|CI096494
EST:     GCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: GCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|86887360|gb|CI313263.1|CI313263
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|86869618|gb|CI322104.1|CI322104
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGAT
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCA-Ggttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGAT
EST: gi|86482891|gb|CI125524.1|CI125524
EST:     ATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: ATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|89178910|gb|CI391908.1|CI391908
EST:     TTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88251932|gb|CI349169.1|CI349169
EST:     ACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: ACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|86842125|gb|CI338471.1|CI338471
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTCCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|87030788|gb|CI362002.1|CI362002
EST:     TCAGCA-TGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|86836906|gb|CI347481.1|CI347481
EST:     TCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|86841162|gb|CI342914.1|CI342914
EST:     CATCCCTCTTCTTAGGCACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: CATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88294931|gb|CI522885.1|CI522885
EST:     TCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|44669277|gb|CR282711.1|CR282711
EST:     CCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: CCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88991676|gb|CI019854.1|CI019854
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88524087|gb|CI451973.1|CI451973
EST:     AATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: AATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88437833|gb|CI533790.1|CI533790
EST:     CCAATCNCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGGTGGAGGAGCACTGAACATGATC
genomic: CCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88251358|gb|CI349786.1|CI349786
EST:     CGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: CGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88956575|gb|CI092792.1|CI092792
EST:     TCATCCGTCTTCTNAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|86874617|gb|CI318176.1|CI318176
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCA-TGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88245599|gb|CI245448.1|CI245448
EST:     TCATCCGTCTTCTTAGGGACTATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGGACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|8858787|gb|AU096105.1|AU096105
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|29684916|gb|CB681191.1|CB681191
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88264552|gb|CI368326.1|CI368326
EST:     TCATCCGTCTTCTTA-GGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|86484400|gb|CI127033.1|CI127033
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88906969|gb|CI376041.1|CI376041
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTCCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88971764|gb|CI389001.1|CI389001
EST:     TCAGCATTCCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAACACTGAACATGATC
genomic: TCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|88956530|gb|CI092762.1|CI092762
EST:     TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|15856703|gb|BI809515.1|BI809515
EST:     ACAATTCAGCATT-CCAATC-CTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGA-CACCTGAACATGAT
genomic: ACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCA-CTGAACATGAT
EST: gi|86884778|gb|CI314354.1|CI314354
EST:     TCATCC-TCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTG-ACATGATC
genomic: TCATCCGTCTTCTTAGGGACAATTCAGCATTGCCAATCGCTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC
EST: gi|89175231|gb|CI111750.1|CI111750
EST:     CTGCATATCAG                         GTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGC-CTGAACATGATC
genomic: CTGCATATCAGgttcgtttat ... aatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggctttgatatgggcctctcacaatctcgggctttgttaaaattaatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATCGACGAAGAGAAGGTGATGATGGAGTCGCTCATGTGCCTGAGGCGAGCCG
                                         aattaat  putative branch site (score: 3)
                                 tttgttaaaattaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacacatatacctctgcttgttttctaattaatctcaagagtgttgggctttgatatgggcctctcacaatctcgggctttgttaaaattaatcatccagGTCTCTGGAGAGTACTCCATGATCAAAGCTGGAGGAGCACTGAACATGATCGACGAAGAGAAGGTGATGATGGAGTCGCTCATGTGCCTGAGGCGAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA