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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtatatatatagttgagcaaaatcatctctacttttttttttgaatttatggttcattttttgcaattttatcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 13
gtttgtgtatatatatagttgagcaaaatcatctctacttttttttttgaatttatggttcattttttgcaattttatcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG
|||  || |||| | |  |||   | |   ||||| | ||| ||| ||||| ||   |||    ||  | ||||||||||| |||| |||||| | || || |||||||| || |||||||||||||| ||||| || ||||| |||
gttcttgcatatttctgattgccgatagctatctcaattttgtttgttgaacttgaagtttgactt--gtaattttatcagCCATATGCTGCAGCAAAGGCTAGAGAATACCTCGACAAGCCTGCTTTGCATGAAACAATGGTTAAG

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 13
gtttgtgt-atatatatagttgagcaaaatcatctctacttttttttttga-atttatggttcattttttgcaattttatcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG
|| ||| | | |  | |||| ||  |  ||  |   | || ||||       ||| |     |||||| ||    ||| |||| | || |||||| | |||||  |||||||||||||||| |||||| |||||||||| ||||| |||
gtgtgtttgaaacttgtagt-gactatgatactgcttcctattttacacatcattcacaaggcattttctgt--ctttctcagCCTTATGCTGCAGCAAAAGCTCGAGAATATCTTGACAAACCTGCTATACATGAGACAATGGTTAAG

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 13
gtttgtgt-atatatatagttgagcaaaatcatctctacttttttttttga-atttatggttcattttttgcaattttatcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG
|| ||| | | |  | |||| ||  |  ||  |   | ||  |||       ||| |     ||||||  |    ||| |||| | || |||||  | |||||  |||||||||||||||| |||||| |||||||||| ||||| |||
gtgtgtttgaaacttgtagt-gactatgatactgcttcctaatttacacatcattcacaaggcattttccgt--ctttgtcagCCTTATGCTGCGGCAAAAGCTCGAGAATATCTTGACAAACCTGCTATACATGAGACAATGGTTAAG

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 13
------gtttgtgtatatatatagttgagcaaaatcatctctacttttttttttg--aatttatggttcattttttgcaatttta-----tcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG
       |     |   |  ||  || |    | |  | ||| || |||     |  |    ||  || ||||  |   | ||||     |||| | || || ||| | || || ||||| |||||||||||||||||| | |||||||| |||||||||
gtgatcatcatctttcttgcatgattcattggattggtgtcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcagCCCTATGCAGCAGCAAAGGCAAGAGAGTATCTTGACAAGCCTGCTATCCATGAGACAATGGTCAAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 154

TGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGACCTACAGgtttgtgtat ... attttatcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

TGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGACCTACAGgtttgtgtat ... attttatcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 157

TGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGACCTACAGgtttgtgtat ... attttatcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 137

TGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGACCTACAGgtttgtgtat ... attttatcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcatctctacttttttttttgaatttatggttcattttttgcaattttatcagTCATACGCTGCAACTAAAGCGAGAGAATATCTTGACAAGCCTGCTTTACATGAGACGATGGTCAAG
                                              ttttatc  CT-rich tract
            ttttttttttgaattt  TA-rich tract