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'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATACTATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAGgtaatgtactttggtgtctttgaaaactttgtgtatacttgcagatctaaatccatatgattctgcttatttagaaccagtcattgaattgtttggttgc...

Basic information

species Zea mays
transcript GRMZM2G071304_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071304_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os10g34750.2 (Oryza sativa), 5'ss of exon 14
GCATACTATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAGgtaatgtac-tttggtgtctttgaaaactttgtgtatacttgcagatctaaatccatatgattctgcttatttagaaccagtcattgaattgtttggttgc-
||||||||||| ||||  ||||||||| |||| ||||||||||||||||| ||||||||||||  |   |      |||||  ||    ||| |  | |  |  ||   | | | |  ||  |    |||   | || ||| ||  | || |||     
GCATACTATAGGTTTGCTGACACAATGGACCCAGATGTGTGGTTTGAGCCTTCAGAGgtaatgcccaccttaaacttttgactaccgactgtttcttagttgtactcg-tacttcttgttaggggcttttgccatcactcactgc-tggtctggaactc
















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|67020482|gb|CO449231.1|CO449231
EST:     ATAGATTTGCCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAG                         GTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCT
genomic: ATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAGgtaatgtact ... cttttcacagGTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCT
EST: gi|211137634|gb|FL282503.1|FL282503
EST:     ATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAG                         GTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCT
genomic: ATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAGgtaatgtact ... cttttcacagGTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCT
EST: gi|18661332|gb|BM501358.1|BM501358
EST:     ATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAG                         GTCTGGGAGGTCAAAGCTGCCGATCTGGGCATAAGCCCTGTACATCGTGCT
genomic: ATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAGgtaatgtact ... cttttcacagGTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCT

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: 47 (upstream exon), 46 (downstream exon)
Score: 119

GCATACTATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAGgtaatgtact ... cttttcacagGTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 31

GCATACTATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAGgtaatgtact ... cttttcacagGTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 43

GCATACTATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAGgtaatgtact ... cttttcacagGTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 19

GCATACTATAGATTTGGCGACACAATGAACCCCGATGTGTGGTTTGAGCCATCAGAGgtaatgtact ... cttttcacagGTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAG