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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTGgtaatttgaattatctgcaaccctgaagatgttgtgtgatatctcttgaagacctaagtcataacgttgtgctagatcctctcttttttaccctaccaca...

Basic information

species Zea mays
transcript GRMZM2G140328_T02
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 20
CTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTGgtaatttgaattatctgcaaccctga-agatgttgtgtgatatctcttgaagacctaagt-cataacgttgtgctagatcctctcttttttaccctaccaca
|| || |||| ||||||||| ||||||   ||||| |||||||||||||| || || |||||||||||||||||  |||| |||||||||||||| |||||||||   | ||||||||||  ||| |||     |    ||| | ||       |  ||     || ||    |  |   |  | |   ||  | || |  
CTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTTTTCCCATTCAACTCAGAGAAAAAAAGAGGCGGGGTTGCAGTGCATCTGgtaattcataatatctgcaactttgacagaccccttcccctattttttttcttattgtgtatggtacattaccatgtaaaatggcatgcctagtcaacta--

upper sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA17G06520.1 (Glycine max), 5'ss of exon 22
CTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTGgtaat-------------ttgaatt---atctgcaaccctgaagatgttgtgtgatatctcttgaagacctaagtcataacgttgtgctagatcctctcttttttaccctaccaca----------------------------------
|| || ||||| ||  |     | ||||  |||||||| ||| |||||||||| || ||||| ||||| ||||||||||| || ||||||       |||||||             || ||||   || || ||   |   | |  |||   | |    ||   || ||||   || |  |  |  |  |   | | || |||  | | ||| |                                  
CTTGGGATGAATTTTGACACTGCCAGATCAAAGTCATCAATTATTCATGTATTCCCATTCAATTCAGACAAAAAGCGAGGAGGAGTTGCAACATGGGTGgtaatagcttgttgccattttaattcaaatatgtaaattttttgcttctgttctaaactgattagggagctaatatattatataataatgtactatattttgtttgtcat-ccagaccactattgctaataattttatacttttccgcag

upper sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA13G00420.1 (Glycine max), 5'ss of exon 20
CTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTGgtaat-------------ttgaatt---atctgcaaccctgaagatgttgtg------tgatatctc-ttgaagacctaagtcataacgttgtgctagatcctctcttttttaccctaccaca----------------------------------
|| || ||||| ||  |     | ||||   | ||||| ||| |||||||||| || ||||| ||||| ||||||||||| || ||||||   |   |||||||             || ||||   || || ||   |   | |  |||       |||||  |  ||   || ||||   || |  |  |  |  |   | ||||  ||  | | ||| |                                  
CTTGGGATGAATTTTGACACTGCCAGATCAGACTCATCAATTATTCATGTATTCCCATTCAATTCAGACAAAAAGCGAGGAGGAGTTGCAACACGGGTGgtaataccttgttggcattttaattcaaatatgtaatttttttgcttctgttctaaactgatacattattagggagctaatatattatatgataatgtactatatcttgcttgtcat-ccagaccactattgctaataattttatacttttccgcag

upper sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 20
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 21
CTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTGgtaatttgaat-tatctgcaaccctgaagatgttgtgtgatatctcttgaagacctaagtcataacgttgtgctagatcctctcttttttaccct-accaca-------
 |||| ||||| ||  ||| || ||||    | || || ||||| ||||| || ||||||||||||||||||||| ||||||| |||||||| ||   |||||||   || | ||      | |    ||| | ||         |||  |||  ||||   ||     || | ||     | || | ||   | |  |||       
TTGGGGATGAAGTTTGATGTAATAAGAGAAGAATCCTCAATTCTCCATGTTTTCCCTTTCAACTCAGAGAAAAAGAGAGGTGGTGTTGCAGTACA---Ggtaattgatatgtttccatggtctta---atgctatga------ctttgttgacagaagttccaaaaacctgttggacataattttgtgtaagttgaaaacataggatt

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: 199

CTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTGgtaatttgaa ... ttttttgaagGATGGCCCTGAAGTCCATATACACTGGAAAGGAGCAGCTGAAATCATTTTGGATTCATGCACAAGCTGGCTTGACACTGATGGTTCGAAGCACTCAATGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 31

CTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTGgtaatttgaa ... ttttttgaagGATGGCCCTGAAGTCCATATACACTGGAAAGGAGCAGCTGAAATCATTTTGGATTCATGCACAAGCTGGCTTGACACTGATGGTTCGAAGCACTCAATGA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 11

CTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTGgtaatttgaa ... ttttttgaagGATGGCCCTGAAGTCCATATACACTGGAAAGGAGCAGCTGAAATCATTTTGGATTCATGCACAAGCTGGCTTGACACTGATGGTTCGAAGCACTCAATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

CTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTGgtaatttgaa ... ttttttgaagGATGGCCCTGAAGTCCATATACACTGGAAAGGAGCAGCTGAAATCATTTTGGATTCATGCACAAGCTGGCTTGACACTGATGGTTCGAAGCACTCAATGA