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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctctagttccatgtttctaacttatgtttcattttgaagtcctaagctttcacaaggtgattacacccgttcacttttctactggcag

Basic information

species Zea mays
transcript GRMZM5G835213_T01
intron # 9
splice site 5'
intron type U2

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|24934275|gb|CA452493.1|CA452493
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|71436375|gb|DR817425.1|DR817425
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|71324258|gb|DR798829.1|DR798829
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|31361403|gb|CD445760.1|CD445760
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|22546594|gb|BU098905.1|BU098905
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|22545671|gb|BU098030.1|BU098030
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|29544652|gb|CB605032.1|CB605032
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|71317247|gb|DR795307.1|DR795307
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|194717059|gb|FK934212.1|FK934212
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|5268356|gb|AI770320.1|AI770320
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|26456698|gb|CA828281.1|CA828281
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTT-GTAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|32850339|gb|CD990020.1|CD990020
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
EST: gi|32866442|gb|CF006124.1|CF006124
EST:     GATGCTCAAAGTGCGATAAATGACTTGAATG                         GGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG
genomic: GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTG

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: 39 (upstream exon), 49 (downstream exon)
Score: 1190

GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTGCTAATGCTGGTGAAGAGAAACAGATTCTGGACACTAAGGTTGACCTGTC


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 534

GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTGCTAATGCTGGTGAAGAGAAACAGATTCTGGACACTAAGGTTGACCTGTC


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 491

GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTGCTAATGCTGGTGAAGAGAAACAGATTCTGGACACTAAGGTTGACCTGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1697

GATGCTCAAAGTGCGATAAATGACTTGAATGgtgtgttctc ... ctactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTGCTAATGCTGGTGAAGAGAAACAGATTCTGGACACTAAGGTTGACCTGTC