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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA

Basic information

species Oryza sativa
transcript LOC_Os02g47860.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143804_T01 (Zea mays), 3'ss of exon 1
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaa---agatcttaatacaaaccaaacattcatttcgcaat-ttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
     | || |    |   |  || ||   | |     ||   | |   | |    | | |     | || |  |      |   |||        ||||| || |  ||  | |  | |||   ||     |   | |   | || |      || || |||| ||||||| |||||||||  ||||| ||||||||||| || ||||| || ||||| |||||||| ||||| || |||||||||||||||| |||||| |||||||||||||
----gtacaacgagctagccaggaacccgaagaaataattgatcaaatctctcaaacgataggttgaaatttccaacttggctttacacattaggagcaatcttgtggttcatgttaacagtgaattggctcttactgtaattggtgtggtttaatcaaagatgacattttt-agGTTTATCTAATGTACAAGGCTTTCATCGAACCAGATTTACAGACCGCACATATTAAAATCATTAACAAGTTCAACCCATGCTCAGGTTTCCAAAATCCTA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 4
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                            ||  ||   ||| | |||     ||  | |       | ||   || | |   |  ||  ||   | ||  | || || || |    ||  |||| ||||||  | ||     ||| |||||||||||||||||| ||||| ||||||||||| || ||||| ||| |||| |||||||| || || |||||||||||||||||||| |||||||||||||||||||
-------------------------------------------gtaggttgaattttc-caacttggctatacattttatgagca---atgttgttgtccattgttaaca-gtgaattacctcttactgtaattggtgtggtttaatgaaat-----atgacatttttcagGTTTATCCAATGTACAAGGCTTTCATCGAACCAGATTTGGAGACCGCACATATTAAGATCATCAACAAGTTCAACCCATTTTCAGGGTTCCAAAATCCTA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G14110.1 (Glycine max), 3'ss of exon 4
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                                                                     |||||      ||   |  ||||    | |  ||    |||     || ||||||     |   | | ||   |     ||||||||| ||||| ||||| ||||| || || ||||||||  | ||||||||||| |||||||| |||||||| ||||| |||||  | || ||||| | |||||
------------------------------------------------------------------------------------gttcatacgtttataattcctttggtctttttatacagatttggaaaatatgtgtttccagaagtgcttaagtttaaacattttcagGTGTATCCAATGTACAAGGCATTTATCGAGCCAGATCTCCAGACAGCACACATAAAAATCATCAACAAATTCAATCCATTTACTGGATTCCAGAGTCCTA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G09080.1 (Glycine max), 3'ss of exon 4
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaattt--atattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                                     ||| |||    ||||| |    | |      |||  ||| | | |||  | |  ||| || | ||  | ||    || |   || |  | |||||| |  ||     |  | |||| ||||| ||||| |||||||| ||||| |||||||||||  |  | ||||| ||| ||||||| || |||||||| || |||||||| || ||||| ||||| |
---------------------------------------------------gtttttcact---gatctcatgttata------atttttttaggacttttgaaaacttgcatctgtaaga-ctaaggcacctg-ctataatttttaactat-tgttttgtttccttttgcagGTGTATCCTATGTATAAAGCTTTTATTGAGCCAGATCTCAAAACAGCTCATCTAAAAATTATTAACAAGTTTAATCCATTCTCTGGATTCCAGAATCCCA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G09660.1 (Glycine max), 3'ss of exon 4
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                                                                   ||| | |||   ||||  | |  | | | ||||  |  |||   |   |||||| ||  |  |   | | ||   |     ||||||||| ||||| ||||| ||||| || || ||||||||  | |||||||||||||||||||| |||||||| ||||| |||||  | || ||||| | |||||
--------------------------------------------------------------------------------gttcatac-ttttataattcctttcatctttttata-cagatttagaaaatatctgtatttctagaagtgcttaagtttaaacattttcagGTGTATCCAATGTACAAGGCATTTATCGAGCCAGATCTCCAGACAGCACATATAAAAATCATCAACAAATTCAATCCATTTACTGGATTCCAGAGTCCTA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 3
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatc---catctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                 ||  |||| | |||  | ||||      |||| | |   |||  |   |||  | ||        ||| ||| |  || || || || | ||  |     |||| |  || ||| |||                    ||||| ||||| ||||| |||||||| |||||||||||  | || ||||||||||||||||| |||||||| ||||| |||||| | || || || || || |
--------------------------------gtgt-tttcacttatactatgtta----gaaagttttctttacttaatgaactgttatggtagccctta-attattcatataaagcatttattgtacttctcatcagctttcttttaca--------------------cagGTATATCCTATGTACAAGGCTTTTATTGAGCCAGATCTACAAACAGCACATATAAAAATCATCAACAAATTCAATCCATTCACTGGATTTCAGAACCCCA

upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0010g01080.t01 (Vitis vinifera), 3'ss of exon 3
gttgcttcacctttttgaacttgaccctatatatgcctttcccctatcttttgtttccacaaaagatcttaatacaaaccaaacattcatttcgcaatttatattttgtatgtatagtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                                                                  |  |   ||  |||      | | | |||   |||    || |   |  | | |  ||||||   || |       | ||| | ||           ||   ||||| ||||| ||||| |||||||| |||||||||||  |    ||||||||||||||||| | ||| ||||||||||||||| | || || || | ||| |
-----------------------------------------------------------------gttctttcacttaccctctgctaaatacgccccttaagaattttgactggattttgcttttcaagaattt------ctcaactacatt-------cttttaaacagGTATATCCAATGTACAAGGCTTTTATTGAGCCAGATCTCGGAACAGCACATATAAAAATCACCAATAAGTTCAACCCATTCACTGGATTTCAGAGTCCCA

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: 47 (upstream exon), 69 (downstream exon)
Score: 13

CACTGGTGGTGTTCATTTTGACCTGGTGAAGAGGGTCCTGAGGGACATACAGAGAGCTGGCCAGGAGCCTGAGGAAATAATTCATCAGATATCTGAAACGgttgcttcac ... catttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatctttttcatccatctgtgttgtttaacaagatgaacgatggcatttttcagGTTTATCCGATGTATAAGGCTTTCATTGAGCCAGACTTGCAGACAGCACATATAAAAATAATCAACAAGTTCAACCCATTCTCAGGGTTCCAAAATCCTA
                        gtttaac  putative branch site (score: 13)
                                             catttttc  putative PPT
     tttttcat  TA-rich tract