Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGAAGGGAAAAGTAGAGAGTATCTATTGAGTTGTGATCTTCTATGGGGCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaaggcttatctacactgtctaatgacattatatttttgagcctaaatatttcatatgttgcgtgtaaatgctatgttactgatatcatagggct...

Basic information

species Zea mays
transcript GRMZM5G816015_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816015_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g36490.1 (Oryza sativa), 5'ss of exon 13
TTGTGAAGGGAAAAGTAGAGAGTATCTATTGAGTTGTGATCTTCTATGGGGCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaaggcttatctacactgtctaatgacat---tatatt-----tttgagcctaaatattt-catatg-ttgcgtgtaaatgctatgttactgatatcatagggct--------------------------
|  |||||| ||||  ||||| ||||||||||||||||||||||||||||  ||  |||| |||||||| |||||||||||| |||||||||  || ||||| | | |  | ||  || | || | |  | |||   |   ||     ||||| || | | |||| || ||| ||   | ||  |  |        ||  | | |    |                          
TGATGAAGGAAAAAACAGAGAATATCTATTGAGTTGTGATCTTCTATGGGTTCTTGAGCATTACCAGAAGTGTGACCGTGTAGTTACTCCCACATTGAAGgtaacagaaacataattatattgccgagcggcatgtttcggttgatgatttgaaccaataaattttcacatgattttatatactttttccacagtcgagcttacacatttatcttctttttattaaatgtatgcag
















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|20300806|gb|BQ163749.1|BQ163749
EST:     GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAG                         ACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG
genomic: GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaagg ... gtatttgcagACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG
EST: gi|87153556|gb|DY398345.1|DY398345
EST:     GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAG                         ACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG
genomic: GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaagg ... gtatttgcagACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG
EST: gi|87153603|gb|DY398392.1|DY398392
EST:     GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAG                         ACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG
genomic: GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaagg ... gtatttgcagACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG
EST: gi|211263861|gb|FL390541.1|FL390541
EST:     GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAG                         ACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG
genomic: GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaagg ... gtatttgcagACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG
EST: gi|19058079|gb|BM736746.1|BM736746
EST:     GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAG                         ACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG
genomic: GCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaagg ... gtatttgcagACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG

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), 45 (downstream exon)
Score: 172

TTGTGAAGGGAAAAGTAGAGAGTATCTATTGAGTTGTGATCTTCTATGGGGCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaagg ... gtatttgcagACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 43

TTGTGAAGGGAAAAGTAGAGAGTATCTATTGAGTTGTGATCTTCTATGGGGCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaagg ... gtatttgcagACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 82

TTGTGAAGGGAAAAGTAGAGAGTATCTATTGAGTTGTGATCTTCTATGGGGCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaagg ... gtatttgcagACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 61

TTGTGAAGGGAAAAGTAGAGAGTATCTATTGAGTTGTGATCTTCTATGGGGCCTCCAGCACTACCAGAAATGTGACCGTGTAATTACTCCCATGTTCAAGgtcataaagg ... gtatttgcagACTATTGAGGCTCTCTTCAGTAAAAAGGTTTTCTTGAACAAGGAG