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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAAGAGCTTATCGAATGGAATGTTCTTCCTTGATCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTGgtctgttctcagcccatatacattcagttgactattccgtaacctcatttctgactaatcattttgtcttcttcaccaatgactaatctactatttgtttttgaacataag

Basic information

species Zea mays
transcript GRMZM2G382341_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G382341_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g48740.1 (Oryza sativa), 5'ss of exon 13
GACAAGAGCTTATCGAATGGAATGTTCTTCCTTGATCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTGgtctgttctca-gcccatatacatt--cagttgactat--tccgtaacctcatttctgactaatcattttgtcttcttcaccaatgactaatctactatttgtttttgaacataag-
|||||||||||||| ||||||  ||| |||||||| ||||||||  ||||||| || |||||||| ||||||||||||||||| || ||||||  ||||||||||  | || | | |  |||   | ||||  ||  |   | ||    | | |   ||  | ||| |    |   | || || || ||  |||||||  |||  |   |    
GACAAGAGCTTATCAAATGGACGGTTTTTCCTTGAACTTCTTAGTGCAGTACAACCGAGGGTTGTCAACTGGAAAGTTGTTACAAAGGGGGAAGATGgtctgttcatatgcacgtttgaattactatttgatgataatttctgactgtttatatatgtatccttttggaaaaccgtagcattggctgattcactatttcctttcaattctgcag

upper sequence: GRMZM2G382341_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA14G00820.1 (Glycine max), 5'ss of exon 12
GACAAGAGCTTATCGAATGGAATGTTCTTCCTTGATCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTGgtctgt------tctcagcccatatacattcagt--tgacta---ttccgtaacctcatttctgactaatcattttgtctt---cttcaccaatgac--taatctactatttgtttttgaacataag-----------------------------------------
|| ||||   | ||   |||  | ||||||||||| ||| | ||  | ||  ||||||||||||| |||||||   |||||||||||||||| |||||| |||      | |||  |  |  | |   |||  || |||   ||| |    |   | | | | |   ||||  |  ||    || || | ||||  |||| |  | |   | | | | | || |                                         
GATAAGAATCTTTCTGGTGGCGTTTTCTTCCTTGAGCTTTTGAGTGCTGTGGAGCCAAGGGTTGTCAACTGGAGTCTTGTTACTAAAGGGGAGACTGgtatgtcaactctgtcattctgttgagaaatagtgctggctagaattctgcttgcaactctttaatttcacattaagcattatatttgacaattgacattaatatgatgtgaatatgttatcttatgagcaacaattgaaatggtcaaatttgtcatatgaattgcag

upper sequence: GRMZM2G382341_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv12s0059g00560.t01 (Vitis vinifera), 5'ss of exon 12
GACAAGAGCTTATCGAATGGAATGTTCTTCCTTGATCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTGgtctgttctcagcccatatacattcagttgactattccgtaacctcatttctgactaatcattttgtcttcttcaccaatgactaatctactatttgtttttgaacataag
||||||| | | |||||||| || ||||||||||| ||||||||  | ||  ||||||||||||| ||||||||  || |||| || || |||| ||||  ||  | |    | | |     | ||   | || | ||         ||||  ||| ||||  | ||   ||   || |   |  |     |  |||           
GACAAGAACCTTTCGAATGGGATTTTCTTCCTTGAGCTTCTTAGTGCTGTGGAGCCAAGGGTTGTCAACTGGAACCTTATTACAAAGGGTGAAAGTGgtacgtcattatagaaaacaaggaaattttgat-tttcatagttcttgagctga--aataatttatttttgggcatagattatggacattaagatcatttcat--------

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), 42 (downstream exon)
Score: 34

GACAAGAGCTTATCGAATGGAATGTTCTTCCTTGATCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTGgtctgttctc ... tgaacataagATGAGGACAAGAAGCTGAATGCTACCTACATCATTAGTGTTGCAAGGAAGATTGGATGCTCTGTGTTTCTGTTGCCAGAGGACATCATTGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 89

GACAAGAGCTTATCGAATGGAATGTTCTTCCTTGATCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTGgtctgttctc ... tgaacataagATGAGGACAAGAAGCTGAATGCTACCTACATCATTAGTGTTGCAAGGAAGATTGGATGCTCTGTGTTTCTGTTGCCAGAGGACATCATTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

GACAAGAGCTTATCGAATGGAATGTTCTTCCTTGATCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTGgtctgttctc ... tgaacataagATGAGGACAAGAAGCTGAATGCTACCTACATCATTAGTGTTGCAAGGAAGATTGGATGCTCTGTGTTTCTGTTGCCAGAGGACATCATTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 187

GACAAGAGCTTATCGAATGGAATGTTCTTCCTTGATCTTCTTAGCACAGTACAGCCAAGGGTTGTGAACTGGAAAGTTGTTACTAAAGGGGAAACTGgtctgttctc ... tgaacataagATGAGGACAAGAAGCTGAATGCTACCTACATCATTAGTGTTGCAAGGAAGATTGGATGCTCTGTGTTTCTGTTGCCAGAGGACATCATTGAG