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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgccatcgtccctcctcccttccttatcctcttccgtcccaccgcacctggtttgttcctcctgcccataaaccccggagaaaccctagcgagcggcgattgacatttgattgtgtgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG

Basic information

species Zea mays
transcript GRMZM2G101250_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101250_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g09860.1 (Oryza sativa), 3'ss of exon 1
gtaagcgccatcgtccctcctcccttccttatcctcttccg---tcccaccgcacctggtttgttcctcctgc-ccataaaccccggagaaaccctagcgagcggcgattgacatttgattgtgtgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG
||| || ||      | ||   ||   || |  | |  ||    | |||| |    |  | || | ||  ||  ||||||| ||| ||||||||||| |          | |||  ||||| |   ||  |||||| ||||||| |||||||||||| ||||| ||  |||| ||||||||| |||| || ||||||||||||||||
gtaggctccccatggcttctctcccctctcaatcgcggccaaaattccactgggttt--tctgctacttttgagccataaatccccgagaaaccctaac----------taacaagtgattttccatc--gcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCCAACCTCGTCGTCATCAACCCAG
















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|211065125|gb|FL021092.1|FL021092
EST:     CACGTCCAGGCGTTCCCGTGCCGGTGGCCAAGCCAGCAGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
EST: gi|148934269|gb|EC878292.2|EC878292
EST:     CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
EST: gi|211065129|gb|FL021096.1|FL021096
EST:     CACGTCCAGGCGTTCCCGTGCCGGTGGCCAAGCCAGCAGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
EST: gi|211065122|gb|FL021089.1|FL021089
EST:     CACGTCCAGGCGTTCCCGTGCCGGTGGCCAAGCCAGCAGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
EST: gi|211065128|gb|FL021095.1|FL021095
EST:     CACGTCCAGGCGTTCCCGTGCCGGTGGCCAAGCCAGCAGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
EST: gi|211065119|gb|FL021086.1|FL021086
EST:     CACGTCCAGGCGTTCCCGTGCCGGTGGCCAAGCCAGCAGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
EST: gi|211067851|gb|FL021097.1|FL021097
EST:     CACGTCCAGGCGTTCCCGTGCCGGTGGCCAAGCCAGCAGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
EST: gi|211065127|gb|FL021094.1|FL021094
EST:     CACGTCCAGGCGTTCCCGTGCCGGTGGCCAAGCCAGCAGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
EST: gi|211065118|gb|FL021085.1|FL021085
EST:     CACGTCCAGGCGTTCCCGTGCCGGTGGCCAAGCCAGCAGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
EST: gi|91056341|gb|EB166759.1|EB166759
EST:     CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATG                         GACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC
genomic: CACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCC

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: 150

CGTTGTCTTCTCTAGCGACGGCGAGGCTTGAGCGCTCACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 108

CGTTGTCTTCTCTAGCGACGGCGAGGCTTGAGCGCTCACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

CGTTGTCTTCTCTAGCGACGGCGAGGCTTGAGCGCTCACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 68

CGTTGTCTTCTCTAGCGACGGCGAGGCTTGAGCGCTCACGTCCCGGCGTTCCCGTGCCGGTGGCCAAGCCAGCGGCCGACGAGATGgtaagcgcca ... tgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccccggagaaaccctagcgagcggcgattgacatttgattgtgtgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG
                                  atttgatt  TA-rich tract