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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACACGGTCACTGGGTTTTTGTTGGCTGGAGTTGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacctcaactttctaacgtgcaaagctgtttaatttttccatcaatgtcaggctgcttttattctgactatatataaggggaacatcgcgtgaca...

Basic information

species Oryza sativa
transcript LOC_Os02g57854.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57854.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G02620.1 (Arabidopsis thaliana), 5'ss of exon 3
GACACGGTCACTGGGTTTTTGTTGGCTGGAGTTGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgta-ataacctcaactttctaacgtgc-aaagctgtttaatttttccatcaatg--tcaggctgcttttattctgactatatataaggggaacatcgcgtgaca---
||||| ||   ||| |||||| ||||||||||||| ||||||||  | ||||  |||||||||||||| || || |||   ||||  |      ||||   ||   |    | |     |||| ||| ||   |||  ||| |      ||||      ||| |  ||| || |   |   |||||   
GACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAAgtatgtttttctaactcaatatgatcttgaggaaagataatcttttcaatcatgaatcaag------ttatgtcacttatctcaaagtggtat-ccttttgacaaaa

upper sequence: LOC_Os02g57854.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv05s0062g00210.t01 (Vitis vinifera), 5'ss of exon 3
GACACGGTCACTGGGTTTTTGTTGGCTGGAGTTGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacctcaactttctaacgtgcaaagctgtttaatttttccatcaatgtcaggctgcttttattctgactatatataagggga-acatcgcgtgaca-
|||||  | |||||||||||| |||||||||| || ||||||||  || ||| |||||||||||| || ||||||||    ||||        |  ||  |       | ||   | ||  ||    |||    | ||     |    || |   |  | |||| |  | | |||   | |   
GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAAgtacgtttacgagtttagttgatcctagagtattataggttgcttatc--ctttagttgattgaatttttaggttaacataaagatataaatcaaattagct
















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|55433570|gb|CV729893.1|CV729893
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88242157|gb|CI242006.1|CI242006
EST:     TTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88353826|gb|CI634617.1|CI634617
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88334071|gb|CI641122.1|CI641122
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|86523723|gb|CI163929.1|CI163929
EST:     AGGAAAAAGACAAATTACCTTATTGTTGATAACT                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: AGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|112785856|gb|EE591550.1|EE591550
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88363322|gb|CI643180.1|CI643180
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88310002|gb|CI657426.1|CI657426
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88339191|gb|CI633762.1|CI633762
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88216147|gb|CI215996.1|CI215996
EST:     CAAATTACCTTACTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: CAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|55433572|gb|CV729894.1|CV729894
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88979436|gb|CI025938.1|CI025938
EST:     TGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|86910935|gb|CI294835.1|CI294835
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|86529211|gb|CI169417.1|CI169417
EST:     GAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: GAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|3761016|gb|C98270.1|C98270
EST:     TGGCAATGTTNATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACANCAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88333055|gb|CI640898.1|CI640898
EST:     TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
EST: gi|88282577|gb|CI403973.1|CI403973
EST:     TTATTGTTGATAACA                         AAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG
genomic: TTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGG

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: 73 (upstream exon), 65 (downstream exon)
Score: 52

GACACGGTCACTGGGTTTTTGTTGGCTGGAGTTGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACAgtaataacct ... catgttacagAAACAACAGTCAAACAAATCGAAGATGCATTTAAGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT




<











<


<