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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtcatgagtgaaagtttcatttgcatactgtttcatttaaggctcaccctaattctatggccagcggattgtgcatgtggccatgcaaacatt...

Basic information

species Zea mays
transcript GRMZM2G368908_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 6
GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtcatgagtgaaagtttcatttgcatactgtttcatttaaggctcaccctaattctatggccagcggattgtgcatgtggccatgcaaacatt
||||||| || ||| | ||||| || ||||||||||| |||||||| ||||| ||||||||||||| |||  ||   | |  |  |  || |||   ||  ||||       |||||||   ||  ||      || |   ||| | |||  ||     
GAGTTGAGCATCTTCTGAGGGATGTCAAGGACACAACAATAAGCACGCTTGCGACAGAGgtaatatttcacaagaatatgcattttcagcctacaagttgctttattat--gccctaat---atatcct-----ttatcattgttgtcattaaag----
















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|149042715|gb|EE047230.2|EE047230
EST:     ACCTTTTTAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGC
genomic: ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGC
EST: gi|32930134|gb|CF034946.1|CF034946
EST:     ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
genomic: ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
EST: gi|148973687|gb|EE024808.2|EE024808
EST:     ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTTGA-GGGACTAGATGCA
genomic: ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTT-GAAGGGACTAGATGCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 235

GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 255

GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC