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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgatgtttaatcattgcactttgtgtatatacttcatagcataaatacttaagatacttcagtttatgctgtccatgtgctagtaattttttggtacttaagatggacaatgaaagttttttgtttactatatttcaattaatttgttgctgtctatgtttactaagtagtttttgggtgtgattttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATAGAAAACTTGGC

Basic information

species Zea mays
transcript GRMZM2G038982_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 3
gtatcgatgtttaatcattgcactttgtgtatatacttcatagcataaatacttaagatacttcagtttatgctgtccatgtgctagtaattttttggtacttaagatggacaa-tgaaagttttttgtttactatatttc-aattaatttg---ttgctgtct-atgtttactaagtagtttttgggtgtgattttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATAGAAAACTTGGC
                                                                                                     || |  |   |   ||  |  ||| | |  | |||||||  || |||||||   |||||| || |  ||| |||||| | |||    |||| | |||| || |||||||||||||||||||| ||||||||||| ||| ||||||||||| ||||| ||||||||||||| ||||| || ||||||||||||  || |||   |
-----------------------------------------------------------------------------------------------------tttatttattcgtctgctacctttgtttcaaatatatttttaaataatttggtattgctgccttacattttctaagtgggttt---atgtgctgtttt-tgcagGGAGTTTTTGGTTGATCTCATGGCTGCTCCCGGTACTCTTATTCCATCAGATGTCTTAAGTTGGAAGGGCAACTCATTAAATTCTAATGCAAGACTCACC

upper sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 4
gtatcgatgtttaatcattgcactttgtgtatatacttcatagcataaatacttaagatacttcagtttatgctgtccatgtgctagtaattttttggtacttaagatggacaatgaaagttttttgtttactatatttcaattaatttgttgctgtctatgtttactaagtagtttttgggtgtgattttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATAG----AAAACTTGGC
        ||| |  | ||    | | ||||| |   |  ||       |  ||||  ||||  | |||||| |   |||  | ||  ||||| |  | | |  | |||    |||  |     |  ||   ||| | | | || |   |     || ||||||     | |    | |       | | |   |  |||||||||||||||||||| ||||||||||| ||  | ||||| ||||| ||||| |||||    || |  | | | || ||  || | |     || | |    
--------gttaaggcttttacatctttgtatttttcttgtat------ttgttaatttact--aatttatg-taatcattggatacaaatttatatgca-tggaaatgattgatgcga-----tcattggatatctctaagtttacccggaaa-gtttatgttgtggtactgacatctc----ctactctgctttcagGGAGTTTTTGGTTGATCTCATGGCTGCTCCAGGGACACTTATCCCAGCTGATATTTTAAGCACCAAGGATAGTGCCTTTAAGCCTTACAATCCCAAGATT----

upper sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 3
gtatcgatgttta-atcattgcactttgtgtatatacttcatagcataaatacttaag-atacttcagtttatgctgtccatgtgctagtaattttttgg-tacttaagatggacaatgaaagttttttgtttactatatttcaattaatttgttgctgtctatgtttactaagtagtttttgggtgtgattttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATAG----AAAACTTGGC
||   |   |||| ||| ||| | |||   | |||  ||  ||   ||   | ||| | || | |  || |||  ||| ||||     ||| | || |   |  || ||     || || | || | |    ||    | ||||   |    |||  ||| | || | ||| |   || |     | || |||       |||||||||||||||||||| ||||||||||| ||  | ||||| ||||| ||||| |||||    || |  | | | || || ||| | |     || | |    
gttaaggcttttacatctttgtatttttcttgtat--ttgttaatttactaatttatgtatgcatgtgtatatcatgtgcatgcctatgtactcttgtaaatggttgaggcaatcattggatgtctcta---ta----agttcacccagaaagtttatgt-tgtggt-actgac--gtctcctactctgctttc------agGGAGTTTTTGGTTGATCTCATGGCTGCTCCAGGGACACTTATCCCAGCTGATATTTTAAGCACCAAGGATAGTGCCTTTAAGTCTTACAATCCCAAGATT----

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: 49 (upstream exon), 49 (downstream exon)
Score: 169

CAGATAGTGTTGGGATTCTATGCAAACTTGTCAAAGGGAGCAATTATACTGGTGGTGATGATGACGATGCTATAAACATAATTAAGATGGACAATGAAAGgtatcgatgt ... ttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATAGAAAACTTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

CAGATAGTGTTGGGATTCTATGCAAACTTGTCAAAGGGAGCAATTATACTGGTGGTGATGATGACGATGCTATAAACATAATTAAGATGGACAATGAAAGgtatcgatgt ... ttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATAGAAAACTTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

CAGATAGTGTTGGGATTCTATGCAAACTTGTCAAAGGGAGCAATTATACTGGTGGTGATGATGACGATGCTATAAACATAATTAAGATGGACAATGAAAGgtatcgatgt ... ttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATAGAAAACTTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

CAGATAGTGTTGGGATTCTATGCAAACTTGTCAAAGGGAGCAATTATACTGGTGGTGATGATGACGATGCTATAAACATAATTAAGATGGACAATGAAAGgtatcgatgt ... ttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATAGAAAACTTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgttgctgtctatgtttactaagtagtttttgggtgtgattttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATAGAAAACTTGGC
 aattaat  putative branch site (score: 164)
                                           ttttttctgt  putative PPT
                                        tgatttttt  TA-rich tract