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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatag

Basic information

species Zea mays
transcript GRMZM2G095348_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 13
TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatca-tgcatttatag
|||||||||  |||| ||||| |||||||| ||||||||||| |||||||||||||||| ||| ||||||||||||||||| || ||||||||||| || |||| |||| |||||| | ||  |   |  | |||   ||  |  || | ||     ||||   |    |   ||| ||| || |||| |||
TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaatattatctattgatatttatagattg-atacttttaacgaattt-catactgaaataactagttttgtcactgtatttttag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 13
TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaat-caagtattattttttcttgggtggaaattttg---tatgtaaaatgtatgagtttactattaaccttttctt-tatcatgcatttatag
 ||||| ||     | ||||||||||| || | |||||||||||||||||| || |||||||| |||||  | || || || || ||||| |||||||| || | | |  | || |  |    |  | |      |||    | |    | ||| |    ||  | ||||  ||||||| | |||           
ATTTGGCGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTACGATTGGGTTGAGTGTAGGTTGATTCGTCGTATTGATGTTAATGTTAAAgtaagtgcttgcatgaggtggcatcagctttctgcttttatttcttcttactgtttcttatttttgttaaatttttcttgtgtcag----------

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 2
TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaat-caagtattattttttcttgggtggaaattttgtatgtaaaatgtatga--gtttactattaaccttttctttatcatgcatttatag
 ||||||||     | ||||||||||| || | ||||||||||||||||||||| |||| ||| || ||  | || || || || ||||| |||||||| || | | |  | || |  |    |  | |     || ||  | ||     | | |  ||||  | ||||  || |    ||  |    |   ||
ATTTGGTGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTATGATTGGGCTGAATGCAGGTTGATTCGTCGTATTGATGTTAATGTTAAAgtaagtgcttgcatgaggtgacatcagct-----ttctgcttttatttcttcttactgtttcttgttaattttgttaaaattttcttgtgtcag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 13
TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaagt-attattttttcttgggtgga--aattttgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatag
 ||||||||     |  |||| ||||| || |  ||||||||||||||||||||||||| ||| || ||  | ||    || || ||||| ||||| || || | |    | ||||  |    ||  ||       | || |   |   ||  ||  ||||| ||| |   | || || ||| ||  |      
ATTTGGTGGCACTCTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGGCTGAATGCAGGTTGATCTATCGCATTGATGTCAATGTGAAAgtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcatt-gtttaatataattttgttattaatcttgtgtcag---

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 13
TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaagt-attattttttcttgggtggaaattttgtatgtaaaatgtatga-gtttactattaaccttttctttatcatgcatttatag
 || |||||    ||  |||| ||||| || |  ||||||||||||||||||||||||| ||| || ||  | ||    || || ||||| ||||| || || | |    | ||||  |    |   ||       |  | |      | |  |  ||||| | | |   | || |||||| ||  |      
ATTCGGTGGCACTTTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGGCTGAATGCAGGTTGATCTATCGCATTGATGTCAATGTGAAAgtaagtactttgattaggtgacatctagttatctgctcttttccttcttattcgttgtttaatttaattttgttatttatcttgtgtcag---

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 13
TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtat----gagtttactatta-accttttctttatcatgcatttatag----------------------------------------------
|||||| ||    ||||| ||||||||||| | ||||||||||||||| ||||| ||||  || || || || || |  | ||| ||||| |  || |||||  ||| | |    || | |||   |||  || || | ||  |  |  | |     | | |    ||| |  || | || |      | || |                                                
TTTTGGAGGAACCTTGTTAGCAATGTGTTCGAATGATTTCATCTGCTTCTATGATTGGGCCGAATGCAGGCTGATTCAACAAATTGATGTCACCGTAAAGgt--atccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 13
TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaagta--ttatttt--ttcttgggtggaaattt---------tgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatag---------------------------------------------
 ||||| ||    ||||| || |||||||| ||||||||||||||||||||||| |||| ||| ||||| || || |  || || || || | ||| |||||    ||  ||  ||   |   ||  | |   ||| |||           ||| |  |||    ||   || ||| |     |||  | | | |  ||  | |                                             
CTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGGCTGAATGTAGGCTGATTCAACGTATTGACGTCACTGTAAAGgtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcag

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), 49 (downstream exon)
Score: 242

TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaag ... gcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 144

TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaag ... gcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaag ... gcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 273

TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaag ... gcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT