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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccccttgttctatttttgttgcttgtttggataatcaacttattcatctctcagacaaatggctcctccagGATTACACTCCGTATTCATGTCAAAAGATTATCTCTGCAACACCTGGTGTTGGTGATCACCATGGTTGCCCTTATCGACATTTTGG

Basic information

species Oryza sativa
transcript LOC_Os07g22400.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G044317_T03 (Zea mays), 3'ss of exon 15
gtaagccccttgttctatttttgttgcttgtttggataatcaacttattcatctctcagacaaatggctcctccagGATTACACTCCGTATTCATGTCAAAAGATTATCTCTGCAACACCTGGTGTTGGTGATCACCATGGTTGCCCTTATCGACATTTTGG--------------
||||| | |     ||   | |||  ||||      |     |  ||||  |  |||  ||| ||| || ||||||||||||||||| ||||||||||||||||| || |||||||||||||| ||||| ||||||||||| || || | ||||||||||||              
gtaagtctc-----ctccatgtgtaacttgaaattgtgccacaagtattacttactctcacacatg-ctgctccagGATTACACTCCATATTCATGTCAAAAGATCATTTCTGCAACACCTGGCGTTGGAGATCACCATGGATGTCCGTTTCGACATTTTGGGTACAATTTGACCC

upper sequence: LOC_Os07g22400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G044317_T02 (Zea mays), 3'ss of exon 15
gtaagccccttgttctatttttgttgcttgtttggataatcaacttattcatctctcagacaaatggctcctccagGATTACACTCCGTATTCATGTCAAAAGATTATCTCTGCAACACCTGGTGTTGGTGATCACCATGGTTGCCCTTATCGACATTTTGG
||||| | |     ||   | |||  ||||      |     |  ||||  |  |||  ||| ||| || ||||||||||||||||| ||||||||||||||||| || |||||||||||||| ||||| ||||||||||| || || | ||||||||||||
gtaagtctc-----ctccatgtgtaacttgaaattgtgccacaagtattacttactctcacacatg-ctgctccagGATTACACTCCATATTCATGTCAAAAGATCATTTCTGCAACACCTGGCGTTGGAGATCACCATGGATGTCCGTTTCGACATTTTGG

upper sequence: LOC_Os07g22400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA08G11130.1 (Glycine max), 3'ss of exon 15
------------------------------------------------------------------------------------------gtaagccccttgttct---atttttgttgcttgtttgg-ataatcaacttattcatctctcagacaaatggctcctccagGATTACACTCCGTATTCATGTCAAAAGATTATCTCTGCAACACCTGGTGTTGGTGATCACCATGGTTGCCCTTATCGACATTTTGG
                                                                                            ||   |  |||| |   ||   |  ||| ||  |   || || |  ||   ||  |   |     |||| |  | ||||| |||||||| ||||| |||||||||||||| ||  |||| ||||| | ||| ||||| |||||||||||||||||| ||||  |
gtaagttttgaatttcccccactgatttatgagatgttttaaatatatttctgttactgatttctattttgaaactaggctttgaaacacaaaatttcaatgtttttgtatgcataatgcatgcatattatgatgagtttcaacaagtaatattttgatggatgttacagGACTACACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGAGATCATCATGGTTGCCCTTATCGAAATTTCAG

upper sequence: LOC_Os07g22400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA05G28150.1 (Glycine max), 3'ss of exon 15
----------------------------------------------------------------------------gtaagccccttgttct---atttttgttgcttgtttg-gataatcaacttattcatctctcagacaaatggctcctccagGATTACACTCCGTATTCATGTCAAAAGATTATCTCTGCAACACCTGGTGTTGGTGATCACCATGGTTGCCCTTATCGACATTTTGG
                                                                              ||   |  |||| |   ||   |  ||| ||| |  ||| || |  ||   ||  |   |     |||| |  | |||||||| ||||| ||||| |||||||||||||| ||  |||| ||||| | ||| ||||| ||||||||||| |||||||||||  |
gtaagttctgaatttccccactgatttatgggatgtttcaaatatatttctgttgctgatttccattttgaaacacaaaatttcaatgtttttgtatgcataatgcatgtatatgatgatgagtttcaacaagtaatattttgatggatgttacagGATTATACTCCCTATTCTTGTCAAAAGATTATTTCATCAACTCCTGGAGCTGGGGATCATCATGGTTGCCCCTATCGACATTTCAG

upper sequence: LOC_Os07g22400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv05s0051g00930.t01 (Vitis vinifera), 3'ss of exon 15
---------------gtaagccccttgttctat--ttttgttgcttgtttggataatcaacttattcatctctcagacaaat--ggctcctcc-----agGATTACACTCCGTATTCATGTCAAAAGATTATCTCTGCAACACCTGGTGTTGGTGATCACCATGGTTGCCCTTATCGACATTTTGG
                 |||  | |     ||   | |   | | | | ||   |   ||   |   |  |   | |||  |  |  |  |||     |||||||||| || ||||| |||||||| ||||| ||  |||| |||||||| || ||||| || ||||||||||||||||||||| |
ctcacctttttacttaaaagtgcttaaaaataagatatgacttcctatatgtgcatgtaaaccaacaacattcaaaacatttttgttttttcctttgcagGATTACACACCTTATTCTTGTCAAAAAATTATTTCATCAACTCCTGGTGTAGGCGATCATCACGGTTGCCCTTATCGACATTTTAG

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: 15 (upstream exon), 36 (downstream exon)
Score: 1

GTTGGCTCTGAGCGATTTGACAAGGAATATGCCTACAGTATCAGGCATAATTATGGAAAGGAAGGAAAACGAACAgtaagcccct ... gctcctccagGATTACACTCCGTATTCATGTCAAAAGATTATCTCTGCAACACCTGGTGTTGGTGATCACCATGGTTGCCCTTATCGACATTTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcttgtttggataatcaacttattcatctctcagacaaatggctcctccagGATTACACTCCGTATTCATGTCAAAAGATTATCTCTGCAACACCTGGTGTTGGTGATCACCATGGTTGCCCTTATCGACATTTTGG
                                              ctcctcc  CT-rich tract
              ataatcaacttatt  TA-rich tract