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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttattgcttgagctatgttttttaagctagtattttatcattctttctgctttgtgctgacatgtacccttttctatgcatcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC

Basic information

species Oryza sativa
transcript LOC_Os03g26960.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G410479_T01 (Zea mays), 3'ss of exon 14
gtatttattgcttgagctatgttttttaagc-tagtattt--tatcattctttctgctttgtgctgacatgtacccttttctatgcatcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC
               |  || |    ||||  | || |||  || || | |    ||||| |  |     ||||     || |||    || ||||||||||| ||||||||||||||||| || |||||||||||||||||| | ||||||||||| |||||||||||||| ||||||||||||||||||||||
---------------gtaatttccaataagtatggtgtttgctaacagtttgctggctttatttttttgggtactgacatccatgtcatatctagGTTACCACTGTGGACAAGTTCCAGGGCCAGCAAAATGATTTCATTTTACTTTCTCTTGTCCGTACCCGTTTTGTGGGTCATCTTCGTGATGTCAGAAGAC

upper sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 12
gtatttattgcttgagctatgttttttaagctagtattttatcattc----tttctgctttgtgctgacatgtaccctttt-ctatgcatcatg-----tagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC
   | |  || ||  |  |      | |||  | |  || ||  ||     ||     | |    | |  | |     ||| || |  || ||       ||||||| |||||||| ||||| || ||||| ||||||||||| || ||  ||||| |||| || || || ||||| || || || |||||||| |||||| 
--gtatgatgttttggacagtagagtaaagagacttcttcattttttaaagttgtgattctcaattaagttatctttgtttactgtaaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT

upper sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 12
-----gtatttattgcttgagcta-tgttttttaagctagtattttatcattctttctgctttgtgctgacatgtacccttttctatgcatcatg-----tagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC
     || ||      | |||  | |     | ||  || | ||||   | |  |  | ||   |   |  || | |  ||||||||  || ||       ||||||| |||||||| ||||| || ||||| ||||||||||| || ||  |||||||||| || || || ||||| || || || |||||||| |||||| 
atgatgttttggacagtagagtaaatagccatcaa--tattttttttgaagttgtgattctcaattaagttatct-ctgttttctataaatgattgctctcagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTCTTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT

upper sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 12
-----------gtatttattgcttgagctatgttttttaagctagtattttatcattctttctgctttgtgctgacatgtacccttttctatgcatcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC
            | ||  ||  |||   |    |         || |  ||||||     |  | |||||| |   |     |   || |||   |     |||| || ||||||||||||||||| || ||||| ||||||||||| ||  | |||||||| || || || || || || ||||| |||||||| |||||  
tttaggtttcgattttggttttttggtatgcaatacccccctaagaaagttatcacagagttagttttgtgttttgactgttctaattttat---ttcctcagGTGACTACAGTGGACAAGTTCCAAGGACAACAGAATGATTTCATATTGCTCTCTCTTGTACGGACACGCTTCGTAGGTCATCTACGTGATGTAAGAAGGT

upper sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 12
----------gtatttattgcttgagctatgttttttaagctagtattttatcattctttctgctttgtgctgacatgtacccttttctatgcatcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC
            ||||  ||      |  |  |||| ||    |   | | ||||   |  |  |    | | || | |    || | | |   |  |  ||||||| ||||| || ||||| || ||||| ||||||||||| || ||| | |||||||| || || || || ||||| || ||||||||||| |||||||
tctgctggcaccatttcctgtgcattcctttattttcaataagggcatgtgtcatggcta-taatcacagatcacttatttgattgtttttttctt-tacagGTTACTACAGTAGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC

upper sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 12
------------gtatttattgcttgagctatgttttttaagctagtattttatcattctttctgctttgt-gctgacatgtacccttttctatgcatcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC
              ||||  ||      |  |  |||| ||   ||   | | ||||   |         |  || |  ||     |||| | |  |      ||||||| ||||| || ||||| || ||||| ||||||||||| || ||| | |||||||| || || || || ||||| || ||||||||||| |||||||
aatctgcaggaaccatttcctgtacattcctttattttcaataaaggcatgtgtcatggctataatcacatcacttagttgattgattttttctttac-----agGTTACTACAGTTGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC

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|2427704|gb|C72167.1|C72167
EST:     ATGTTATTAACAGAAGATGCANGCCATGGAATATCGAACCACCTAGCAAG                         GTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTA
genomic: ATGTTATTAACAGAAGATGCAAGCCATGGAATATCGAACCACCTAGCAAGgtatttattg ... catcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTA




















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: 70 (upstream exon), 73 (downstream exon)
Score: 18

TAAGATTTCGATATTGACCACTTACAATGGTCAGAAGCTTCTTATTCGCGATGTTATTAACAGAAGATGCAAGCCATGGAATATCGAACCACCTAGCAAGgtatttattg ... catcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcattctttctgctttgtgctgacatgtacccttttctatgcatcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC
                     tgctgac  putative branch site (score: 18)
                                    ttttctat  TA-rich tract