Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcattatgagattagatttcaaacccttctccctcttag

Basic information

species Zea mays
transcript GRMZM2G453794_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagccaagcattttgtgtatctatgtactataagt--tcaaattgtcattatgag--attagatttcaaacccttctccctcttag
|||||||||| ||||| || || ||||| || ||| |||||||| | ||||||||||||||||| ||  |||| || ||||||||||||||||||||||||||||| || ||||||| | || || | | |||| |  ||  | | |||   | |  ||   || ||  || |||  | |||| |      
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgt-tactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag----

upper sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G44150.1 (Glycine max), 5'ss of exon 46
CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcattatgagattagatttcaaacccttctccctcttag
|| |    |||||| |  |   ||||||||||||| |||||||  | || ||| | |||||||| |||||||| ||||| ||||||||||| ||||| ||||||| |         | | | ||||| || ||| | |     |  | |||| || |  ||   |  || |   ||     | ||||
CACTCTCATATATTCTTTTGAGTATAAGCAGTTGGTTTATGGCTCTATCCTGGTTGTTTGCTCCATATTTATTCAACCCGTCTGGATTTGAGTGGCAAAAgtaagtatta------tctatttatct-tgaactttgacaggcatgtctcatgattattttccctcacacagtgttt----ttttag

upper sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 48
CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcatta-tgagattagatttcaaacccttctccctcttag
|| |    |||||| |  |   ||||||||||||| |||||||  | || ||| | |||||||| |||||||| ||||||||||||||||| ||||| ||||||| |         | | | ||||| |||| | |   |   |  | |||| | | |   |   ||||   | |    |  | ||||
CACTCTCATATATTCTTTTGAGTATAAGCAGTTGGTTTATGGCTCTATCCTGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaagtatta------tctatttatctttgtattcttcctggcatgtctcatgagtcatgattattttccttcacggtgcttttttag

upper sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 5'ss of exon 43
CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagccaagcattttgtgtatctatgtactataagttcaaattgtcattatgagattagatttcaaacccttctccctcttag
|| |    || ||| | ||    || ||||||||| | |||||  | ||||||||||||||||||||||| || || |||||||| ||||| ||||||||||||| | |      |||| |   | | | |   ||   |     |||    | |   ||||    |       ||  |||| ||||
CACTATCGTACATTCTTCTTAGCATTAGCAGTTGGTTCATGGCTCTTTCTTGGCTTTTTGCTCCCTATTTGTTCAATCCATCTGGTTTTGAGTGGCAGAAgtaagtatcat----ttttctaattttctctctcatggat-----ttgctcatgttttattaaccatttg--ttttaccccttttag

upper sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S67_70V6.1 (Physcomitrella patens), 5'ss of exon 41
CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagccaagc----------attttgtgt--atctatgt-actataagttcaaattgtcattatgagattag----atttcaaacccttctccctcttag------------------------------------------------------------------------
|||||   || ||||| ||| |  | ||    ||| |  ||||  | || ||||| ||||| || ||| | || ||||||||||| || ||||||||||||||||||    |||           |||||| |  ||| |||| |  ||   | | | |  |   || |  |  ||    |  | | |   |    ||||| ||                                                                        
CAGTTACTTACATTTTGCTCACATTCAGTTCCTGGTTCCTGGCGCTTTCGTGGCTCTTTGCGCCATATGTTTTCAACCCATCTGGCTTCGAATGGCAGAAgtaagcactacagctcttgttttcgttttgtattgatcaatgtcatgatgtctgccattcatttgtaagcaacaagtgttacatgatagtttgtgtcctctgaggtcttacgttgtaggagtggtctttcgctcaataatctatttggtcttacaaaatgtaaaattttgatacag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|22545826|gb|BU098200.1|BU098200
EST:     TGG-TTTTTGCT-CCTATTTATTTAACCCATCTGGATTTGAATGG-AGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|67031292|gb|CO460041.1|CO460041
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|211408837|gb|FL082347.1|FL082347
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|50322941|gb|CO518067.1|CO518067
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|6578074|gb|AW244211.1|AW244211
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|32834891|gb|CD974569.1|CD974569
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|211408045|gb|FL038492.1|FL038492
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|67040750|gb|CO467005.1|CO467005
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|32934894|gb|CF039706.1|CF039706
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
EST: gi|26558188|gb|CA830423.1|CA830423
EST:     TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAA                         GATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG
genomic: TGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGG

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: 449

CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 292

CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 276

CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagcc ... tccctcttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA