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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacgttttgagccagcttgcttttttttgttttcttgtacttgtaaaaggtggctaactccggttgagcattttgcagTACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAAAGTTCTGGACTTACAAGATAAG

Basic information

species Zea mays
transcript GRMZM2G137696_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137696_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g48110.1 (Oryza sativa), 3'ss of exon 12
gtatac---gttttgagccagcttgcttttttttgtttt-cttgtacttgtaaa-aggtggctaactccggttgagcattttgcagTACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAAAGTTCTGGACTTACAAGATAAG
|||| |   || | |||||| |    |||     ||| | | | ||  |||  | | ||| ||||||||  || | ||| |||||| ||||||||||| ||  |||| | ||||||||||||| |||| || || |||||||||||| |||||||||||
gtatgctgagtctagagccaacacaatttcgcgagttctacatttaaatgtgtatatgtgtctaactcccatttatcatattgcagCACCCCTGTCTACAGTCCACCTGCTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG
















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|32914811|gb|CF019623.1|CF019623
EST:     GCAGAGAAAGTGAAAGCTTGGCTGGAGGAGAAGGAAAACCTGCAGAAAAA                         CACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAA
genomic: GCAGAGAAAGTGAAAGCTTGGCTGGAGGAGAAGGAAAACCTGCAGAAAAAgtatacgttt ... cattttgcagTACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAA




















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), 46 (downstream exon)
Score: 92

GTTGTGAGTCAAGCAGAGAAAGTGAAAGCTTGGCTGGAGGAGAAGGAAAACCTGCAGAAAAAgtatacgttt ... cattttgcagTACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAAAGTTCTGGACTTACAAGATAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 64

GTTGTGAGTCAAGCAGAGAAAGTGAAAGCTTGGCTGGAGGAGAAGGAAAACCTGCAGAAAAAgtatacgttt ... cattttgcagTACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAAAGTTCTGGACTTACAAGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GTTGTGAGTCAAGCAGAGAAAGTGAAAGCTTGGCTGGAGGAGAAGGAAAACCTGCAGAAAAAgtatacgttt ... cattttgcagTACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAAAGTTCTGGACTTACAAGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

GTTGTGAGTCAAGCAGAGAAAGTGAAAGCTTGGCTGGAGGAGAAGGAAAACCTGCAGAAAAAgtatacgttt ... cattttgcagTACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAAAGTTCTGGACTTACAAGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgttttcttgtacttgtaaaaggtggctaactccggttgagcattttgcagTACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAAAGTTCTGGACTTACAAGATAAG
                            ggctaac  putative branch site (score: 245)
                 ttgtaaaa  TA-rich tract