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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcaattagatttgttgacaaattataaaatgatccatgattctactggaagctgaagaagaaatatattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGT

Basic information

species Oryza sativa
transcript LOC_Os03g58700.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G825524_T01 (Zea mays), 3'ss of exon 7
gtctgcaattagatttgttgacaa--attataaaatgatccat-gattctactggaagctgaagaagaaatatattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGT
|| |||| |  ||  | ||||  |  || ||| | | |   || |||| || ||||| || ||| |  ||| ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| |||||||||||||| |||||||||||||| |||||||||||||| |
gtttgcagtctgaagtattgatgattatgatatattaaattattgattgtattggaa-cttaagtattaatgtattggcagGTGGTTAATTGTAAGGATGACCTTGCACAGTTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGATGAATACCATTTACAAACATTGGAAACATTAT

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 8
gtctgcaattagatttgttgacaaattataaaatgat-ccatgattctactggaagctgaagaagaaatatattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGT
|| |||| |  ||  | ||||        |  ||||| || ||||  || ||||| || ||| |  |||  |||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| || |
gtttgcagtctgaagtattgatgttaatgattatgataccttgatcatattggaa-cttaagtattaatgcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 7
--------gtctgcaattagatttgttgacaaat-------tataaaatgatccatgattctactggaagctgaagaagaaatatattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGT
        |       ||  || | ||  ||  |       ||||   |  || ||   | ||      ||| ||   ||||    |   ||||| || || ||||| ||| |  | || || |  || |||||||| |||||||| ||||||||||| || || |||||||| |||||  | || || || |
gttcggcagctcatttttgcatctattaccatgtcctttcttatagggtt-tcaattcatgtataatctgctaaatctgaaaaccttgaacagGTCGTCAACTGTAAAGATAAGTTGGCTCAGTATTATCTGATGGAGTGCATAATTCAAGTCTTTCCTGATGAGTACCATTTGCAGACTCTTGAGACCTTAT

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 7
gtctg-caattagatttgtt--gacaaatt----ataaaatgatccatgattctactggaagctgaagaagaaatatat--tggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGT
|||||    ||   |  |||  || |  ||    ||  ||   ||| |     |  ||  | ||   |    | ||| |  |   |||| || || |||||||||||||||||||| | |||||| ||||| ||||| || ||||||||||| || || |  ||  | || ||  | ||   ||| |
gtctggtttttctctccgtttagatagtttcagcatccaaccttccgtctacatGTTGTCAACTATTGTCTCACTATGTCTTAAAAGGTTGTCAACTGTAAGGATGAACTTGCACAGTGCTACCTTATGGATTGCATTATTCAAGTCTTTCCTGATGATTTTCACCTTCAAACTCTCGATGTATTAT

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|29628687|gb|CB633698.1|CB633698
EST:     TTGACCTTGACATGTACAAAGAAACTGTCCTTCCGAGGATATTAGAACAG                         GTGGTTAATTGTAAGGATGAACTTG
genomic: TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAGgtctgcaatt ... atattggcagGTGGTTAATTGTAAGGATGAACTTG
EST: gi|29627051|gb|CB632062.1|CB632062
EST:     TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAG                         GTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA
genomic: TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAGgtctgcaatt ... atattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA
EST: gi|58664362|gb|CK053048.1|CK053048
EST:     TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAG                         GTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA
genomic: TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAGgtctgcaatt ... atattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA
EST: gi|58662434|gb|CK051120.1|CK051120
EST:     TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAG                         GTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA
genomic: TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAGgtctgcaatt ... atattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA
EST: gi|58611844|gb|CK039556.1|CK039556
EST:     TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAG                         GTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCAGT
genomic: TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAGgtctgcaatt ... atattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCA-T
EST: gi|29613031|gb|CB618044.1|CB618044
EST:     GACATGTACAAAGAACCTTTACTGCCAAGGATATTAGAACAG                         GTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA
genomic: GACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAGgtctgcaatt ... atattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA
EST: gi|33794974|gb|CF323367.1|CF323367
EST:     TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAG                         GTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA
genomic: TTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAGgtctgcaatt ... atattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATA

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), 67 (downstream exon)
Score: 32

GTAGGCAAAAACCTTCACGTTCTAAGCCAGATTGAGGGTGTTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAGgtctgcaatt ... atattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattataaaatgatccatgattctactggaagctgaagaagaaatatattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGT
                                   aagaagaaatatatt  TA-rich tract