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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcaccactttgtgagccatagctttttatttttgtttttagtaagagcttcttcttgctatcaatgctacttctacggttctacagcgatgtatctgctctatcagaatattttgtgccaatagcagtaacttcatttttgtcctgattgcccttcacctaaaacccag

Basic information

species Zea mays
transcript GRMZM2G160569_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160569_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g44070.1 (Oryza sativa), 5'ss of exon 7
TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcaccactttgtgagccatagctttttatttttgtttttagtaagagcttc-ttcttgctatcaatgctacttctacggttctacagcgatgtatctg----ctctatcagaatattttgtgccaatagcagtaacttcatttttgtcctgattgcccttcacctaaaacccag
||||||||||||||| |  || ||||||||   ||| |||||||| ||||||||||||||||| |   |||||  ||   ||||    |  || || ||||  |  | |  |   |  |  | |||    |  | || |||    | ||   |    |||  |    || |   | || || || |  ||||| |  |   |||  || ||| || ||     |||  | |||| |   
TGTTGATGTTTCTGGGCAACGAGAAATGAGGGACTTCTTCAATGGTATTGTGAGATTGCAGgtatctgccact--gtccaccatgttatgatacttctgttcgtcatgactgtaacacttcttctacatgttatgctactattaatttatgtcagaatatacgatacctttgaaaaaaaatattttctcaatatctttt-tttcgcttatgttctcatgaaaattcgaccaaaaacag-
















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|211266712|gb|FL294975.1|FL294975
EST:     CTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG                         GGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
genomic: CTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
EST: gi|67018103|gb|CO446852.1|CO446852
EST:     CTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG                         GGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
genomic: CTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
EST: gi|31356908|gb|CD441265.1|CD441265
EST:     CGGGAAATGAGATCCTTTTTCAATGGTATTGTGAGATTGCAG                         GGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
genomic: CGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
EST: gi|31356050|gb|CD440407.1|CD440407
EST:     CTGGCCGCCGGGAAATGAGATCCTTTTTCAATGGTATTGTGAGATTGCAG                         GGNTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
genomic: CTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
EST: gi|149085225|gb|EE174733.2|EE174733
EST:     CTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG                         GGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACCAAACC
genomic: CTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
EST: gi|32837541|gb|CD977219.1|CD977219
EST:     CTGGCCGCCGGGAAATGAGATCCTTTTTCAATGGTATTGTGAGATTGCAG                         GGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC
genomic: CTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACC

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: 47 (upstream exon), 48 (downstream exon)
Score: 261

TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 337

TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 210

TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 547

TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcacca ... taaaacccagGGTTCTGGAAGAAGCTTGCCTAGGTCTTGCACCTCACACATGGACAAAACCTCG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAGgtgtgcaccactttgtgagccatagctttttatttttgtttttagtaagagcttcttcttgctatcaatgctacttctacggttctacagcgatgtatctgctctatcagaatattttgtgccaatagcagtaacttcatttttgtcctgattgcccttcacctaaaacccag

- - - - - - - - - - - - -  GAGATC