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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcggtgtcccatctctcatgtccgtttcagaagaaaaccgtattgctgtgttgatgctaattactgatgatgctgaggttcggctatcctggatgcatggctagttcttagagttctagggacaagtacaactattgttaaatagcacgaattcaaggttctgagtatgatttctgtacttcttttgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCTGGGAATTCAAGTCAGTACGTACGATATGCCGGCACCATCGGCATCCATC

Basic information

species Oryza sativa
transcript LOC_Os01g49820.2
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|88390513|gb|CI607549.1|CI607549
EST:     GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GT---                         GCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
genomic: GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAGgttcggtgtc ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
EST: gi|33687572|gb|CF315811.1|CF315811
EST:     GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAG                         GCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
genomic: GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAGgttcggtgtc ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
EST: gi|88294170|gb|CI667144.1|CI667144
EST:     GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GT---                         GCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
genomic: GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAGgttcggtgtc ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
EST: gi|88351936|gb|CI625936.1|CI625936
EST:     GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GT---                         GCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
genomic: GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAGgttcggtgtc ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
EST: gi|2310357|gb|C26512.1|C26512
EST:     GCGGCAA--CANAGGCGNCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAG                         GCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
genomic: GCGGCAAGCCA-AGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAGgttcggtgtc ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
EST: gi|88343234|gb|CI627194.1|CI627194
EST:     GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAG                         GCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
genomic: GGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAGgttcggtgtc ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT

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: 36 (upstream exon), 66 (downstream exon)
Score: 4

AAGGAGAAGTGGAAGAGAAGCCAGAAGGGAGACGACGAGAGATTTGTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGTAAGgttcggtgtc ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCTGGGAATTCAAGTCAGTACGTACGATATGCCGGCACCATCGGCATCCATC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagcacgaattcaaggttctgagtatgatttctgtacttcttttgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCTGGGAATTCAAGTCAGTACGTACGATATGCCGGCACCATCGGCATCCATC
                                          ttttgat  putative branch site (score: 4)
                              tttctgtacttctttt  CT-rich tract
                         tatgattt  TA-rich tract