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

TGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAGgcaagtccatcccttatgtggtatatgtacttctggaaagataaaaacccatctcatgtaaattgatcatgacag

Basic information

species Zea mays
transcript GRMZM2G056975_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g01710.2 (Oryza sativa), 5'ss of exon 7
TGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAGgcaagtccat---cccttatgtggtatatgtacttctgg-aaagataaaaacccatctcatgtaaattgatcatgacag
||||||||||||||| ||||||| |||||||| ||||||||| | |||||||||||||||||||||||| || || |    |    ||||  |||||||  ||||     | ||   |  |||||| || |  |||||| ||| |||
TGTATACAAGGCTTGCCCGAAGGAGCACTTCGCCGCATTATTTTGACTGCATCAGGTGGTGCTTTCAGgtaaatctactgacatacatgttatatatgtttttctactggacattggactccatcttatatccattgatgatgtcag
















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|14206809|gb|BG840487.1|BG840487
EST:     GAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAG                         GGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAA
genomic: GAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAGgcaagtccat ... atcatgacagGGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAA
EST: gi|211496438|gb|FL049443.1|FL049443
EST:     GAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAG                         GGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAA
genomic: GAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAGgcaagtccat ... atcatgacagGGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAA

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: 46 (upstream exon), 47 (downstream exon)
Score: 31

TGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAGgcaagtccat ... atcatgacagGGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 637

TGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAGgcaagtccat ... atcatgacagGGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 539

TGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAGgcaagtccat ... atcatgacagGGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACT


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 48

TGTATACAAGGCTTGTCCGAAGGTGCACTTCGTCGCATTATTCTAACTGCATCAGGTGGTGCTTTCAGgcaagtccat ... atcatgacagGGACTGGCCAGTTGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACT