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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttttggctgtccagctattatactattgaactatagtgattgcaaaaaaaaaaaagaaagttataactaatacatccatattagttgttctgagcttctgcttttctcgatcactctgacttcgtgacaaacacatttgcagttcacttcaaattcaattttggtcaatgacatctttgctctacctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACTGATTACCTGCTCGAGCTACCAACCATATGTTCAAAAGGCCATGAGTACA

Basic information

species Oryza sativa
transcript LOC_Os10g36760.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36760.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G031572_T02 (Zea mays), 3'ss of exon 12
gttggttttggctgtccagctattatactattgaactatagtgattgcaaaaaaaaaaaagaaagttataactaatacatccatattagttgttctgagcttctgcttttctcgatcactctgacttcgtgacaaacacatttgcagttcacttcaaattcaattttggtcaatgacatctttgctctaccta-atctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACTGATTACCTGCTCGAGCTACCAACCATATGTTCAAAAGGCCATGAGTACA-
||  |||| | || |  | || || | | | |||| | ||||| ||   ||  |      || |  | || | ||| | ||  ||  | | | ||||| ||| ||   |     |   || ||     |||||   ||                | ||| || || ||  |  | ||||  |||||||| ||   | |||||||| ||||| ||||||| |||||| || ||||||||||||||| ||   |||| |     |  |||||  || ||| || |   |  |  |  |   || 
gtcagtttggtctatgtatctgttcttccactgaattgtagtggttttgaattatcctc-gatatctttatcaaatgcctctctaacactggctctgatcttttgtgctatcgaagggctgtg-----gtgaccgccaa---------------ccaatccagttctgaac--taacattgttgctctatctgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTTGATCAATCTGTGAAGCTAT-AAGCATGTGCTGCTAGAGTAACCAAGGCAA
















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|86842463|gb|CI335334.1|CI335334
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|3762110|gb|C99358.1|C99358
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|88459544|gb|CI519605.1|CI519605
EST:     TATGGTTATCAGAATGTCAAGAGCAAG                         AACACGACAATGAGCCATTGCTGGGCATTAGATGGAGCATAGCTACTTACT
genomic: TATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|88471937|gb|CI409208.1|CI409208
EST:     CAGATGGTCGATCACATTGATTTATGGTTATCAGAATGTCAGGACCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGGTACTTACT
genomic: CAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|86509840|gb|CI152473.1|CI152473
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|88255907|gb|CI354731.1|CI354731
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|88445264|gb|CI552317.1|CI552317
EST:     GATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|89173586|gb|CI041479.1|CI041479
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|89181004|gb|CI045087.1|CI045087
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|3768110|gb|AU032137.1|AU032137
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|87028775|gb|CI349494.1|CI349494
EST:     ATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGGTACTTACT
genomic: ATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|86842145|gb|CI338486.1|CI338486
EST:     GCAGATCGTCGATCACAGTGATTTATGGGTATCAGGAGGTCAAGAGCAAG                         GACACGACAAGGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|29667886|gb|CB664161.1|CB664161
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|89176609|gb|CI111325.1|CI111325
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|87030148|gb|CI111844.1|CI111844
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|89174046|gb|CI041939.1|CI041939
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|88463972|gb|CI529509.1|CI529509
EST:     ATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: ATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|88264971|gb|CI368745.1|CI368745
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCACAATGTCAAGACCAAG                         GACACGACAATGAGCCATTGCTGGGCACTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|88220720|gb|CI220280.1|CI220280
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|86434153|gb|CI094496.1|CI094496
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|89162466|gb|CI099158.1|CI099158
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|87031114|gb|CI259694.1|CI259694
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|18386498|gb|BM419696.1|BM419696
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCCAGTAGATGGAGCATAGCTACTTAC
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGG-CAGTAGATGGAGCATAGCTACTTAC
EST: gi|29678500|gb|CB674775.1|CB674775
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|86260495|gb|CI066368.1|CI066368
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
EST: gi|88976203|gb|CI024420.1|CI024420
EST:     GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAG                         GACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT
genomic: GCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACT

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: 75 (upstream exon), 75 (downstream exon)
Score: 31

GTGACTCGTCTAATTGTTCATCTCCAGAAGCTGTGAACAAAGTAAGAAAGCAGATCGTCGATCACATTGATTTATGGTTATCAGAATGTCAAGAGCAAGgttggttttg ... ctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACTGATTACCTGCTCGAGCTACCAACCATATGTTCAAAAGGCCATGAGTACA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcacttcaaattcaattttggtcaatgacatctttgctctacctaatctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACTGATTACCTGCTCGAGCTACCAACCATATGTTCAAAAGGCCATGAGTACA
                                           acctaat  putative branch site (score: 31)
                                 tctttgctctacct  CT-rich tract
       ttcaaattcaatttt  TA-rich tract