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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttcttttaaccctctgttatcttccgttgttagaaaagctgcaagtgtagttctcatatgatacttcaaatcttactagGGACAACTGTGAAGTTTGTCTTGGAACAGGACAAAGATGCCTTTATTCGCTTGATTGGTGTCAGTATTCTACAAAGTGGTGCAAATTCTTTTGTGGCACC

Basic information

species Zea mays
transcript GRMZM2G060045_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g01700.1 (Oryza sativa), 3'ss of exon 10
gttg--ttcttttaaccctctgttatcttccgttgttagaaaagctgcaagtgtagttctcatatgatacttcaaatcttactagGGACAACTGTGAAGTTTGTCTTGGAACAGGACAAAGATGCCTTTATTCGCTTGATTGGTGTCAGTATTCTACAAAGTGGTGCAAATTCTTTTGTGGCACC
||||  ||  || ||     |  ||   || |   | |||| |||||||| || | ||||  | |||||| ||  || ||   |||||||||||| |||||||||||||| |||||||||| ||| ||||||||  |||||||| ||||| | || ||||||  |||||||||||||||||| ||
gttggctttgttcaatatcttactaatgtcagaactcagaagagctgcaaatgaatttcttgtctgatacatctcattttgtcagGGACAACTGTTAAGTTTGTCTTGGAGCAGGACAAAGCTGCATTTATTCGTCTGATTGGTATCAGTGTCCTGCAAAGTTCTGCAAATTCTTTTGTGGCCCC

upper sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA11G38160.1 (Glycine max), 3'ss of exon 14
gttgttcttttaaccctctgttatcttccgttgttagaaaagctgcaagtgtagttctcatatgatacttcaaatcttactagGGACAACTGTGAAGTTTGTCTTGGAACAGGACAAAGATGCCTTTATTCGCTTGATTGGTGTCAGTATTCTACAAAGTGGTGCAAATTCTTTTGTGGCACC
  | || | | | |  |    |||  ||  || ||       |||  | |  |  |   | |||| | ||   ||  |   ||| || |||||||||||||| ||||| ||||| |||| | |||||||||| || |||||| | ||| |||| ||||||| ||||  ||||||  | || ||
-gtattttctcatcttttgactat--tcatttatt-------ctgtgaatcca--tgatagatgaaaattt--atgctctcagGTACCACTGTGAAGTTTGTTTTGGAGCAGGATAAAGCTTCCTTTATTCGGTTAATTGGTTTAAGTGTTCTTCAAAGTGTTGCATCTTCTTTCATTGCTCC

upper sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT4G39850.2 (Arabidopsis thaliana), 3'ss of exon 13
gttgttcttttaaccctctgttatcttccgttgttagaaaagctgcaagtgtagttctcatatgatacttcaa--atcttactagGGACAACTGTGAAGTTTGTCTTGGAACAGGACAAAGATGCCTTTATTCGCTTGATTGGTGTCAGTATTCTACAAAGTGGTGCAAATTCTTTTGTGGCACC
       |    |  |||  |  | || | |  | ||      ||  || ||   | |  ||  |  |  | |  || ||   |||||| |||||||||| ||||||||| || || || |  |||||| |||| ||||||||| | ||| |||| ||||||||||||  |||| |  | || ||
------gtaaacatactccatattgttacttgatcagttttattgatagggttccttttctaacaagcaaccatgatttttgcagGGACCACTGTGAAGTATGTCTTGGAGCAAGATAAGGCAGCCTTTGTTCGTTTGATTGGTTTGAGTGTTCTCCAAAGTGGTGCATCTTCTATAATTGCTCC

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 94

GTTCCTAGACTATTTGATAAACAAGGCGGGCAGTTGCTTGCTGTCGCTGTACTTGTTTTCTCTCGGACATGGATCTCTGATCGTATTGCTTCGTTGAATGgttgttcttt ... atcttactagGGACAACTGTGAAGTTTGTCTTGGAACAGGACAAAGATGCCTTTATTCGCTTGATTGGTGTCAGTATTCTACAAAGTGGTGCAAATTCTTTTGTGGCACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GTTCCTAGACTATTTGATAAACAAGGCGGGCAGTTGCTTGCTGTCGCTGTACTTGTTTTCTCTCGGACATGGATCTCTGATCGTATTGCTTCGTTGAATGgttgttcttt ... atcttactagGGACAACTGTGAAGTTTGTCTTGGAACAGGACAAAGATGCCTTTATTCGCTTGATTGGTGTCAGTATTCTACAAAGTGGTGCAAATTCTTTTGTGGCACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

GTTCCTAGACTATTTGATAAACAAGGCGGGCAGTTGCTTGCTGTCGCTGTACTTGTTTTCTCTCGGACATGGATCTCTGATCGTATTGCTTCGTTGAATGgttgttcttt ... atcttactagGGACAACTGTGAAGTTTGTCTTGGAACAGGACAAAGATGCCTTTATTCGCTTGATTGGTGTCAGTATTCTACAAAGTGGTGCAAATTCTTTTGTGGCACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

GTTCCTAGACTATTTGATAAACAAGGCGGGCAGTTGCTTGCTGTCGCTGTACTTGTTTTCTCTCGGACATGGATCTCTGATCGTATTGCTTCGTTGAATGgttgttcttt ... atcttactagGGACAACTGTGAAGTTTGTCTTGGAACAGGACAAAGATGCCTTTATTCGCTTGATTGGTGTCAGTATTCTACAAAGTGGTGCAAATTCTTTTGTGGCACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttgttagaaaagctgcaagtgtagttctcatatgatacttcaaatcttactagGGACAACTGTGAAGTTTGTCTTGGAACAGGACAAAGATGCCTTTATTCGCTTGATTGGTGTCAGTATTCTACAAAGTGGTGCAAATTCTTTTGTGGCACC
                                              tcttact  CT-rich tract
     ttagaaaa  TA-rich tract