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'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggacataagttacgtgagaccatatatgtcaaaatccacatggcacatggctcatttgtgtatacccttctccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACCAATCGTATTTTATCTCGGGCTCTCGCGAGAACCATTAGAAGACTCATGT

Basic information

species Zea mays
transcript GRMZM2G305007_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G305007_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os04g54790.1 (Oryza sativa), 3'ss of exon 20
--------------gtaagttggacat---aagttacgtgagacc---atatatgtcaaaatccacatggcacatggct-----catttgtgt----atac-------------ccttctccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACCAATCGTATTTTATCTCGGGCTCTCGCGAGAACCATTAGAAGACTCATGT
                |||| ||| ||   ||   | ||  ||     || ||| |||  ||| || | | | |||        | |||| |     | ||             |   |   | || |||||||||| ||||||||||||||||| || || |||||||| |||||||| |||||| || | ||||| ||| | || |||||||| |||||| |  |  
gtaagaatggaaatacaagtaggatatggaaatacaagtaggatggaaatgtatatcaggatcgacgttgaatatgatctgtagcttttgagctctcacactaatgcagtaatgctcaccttaacgcagCTTCCACCAGAGTCCCAACAGCAGTTTCTCCTCCTGCCAGCAGATTTAACTAATCGTCTTCTGTCTCGCGCTGTTGCAAGAACCATCAGAAGAATATTCA
















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|78023163|gb|DV491550.1|DV491550
EST:     GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAG                         CTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
genomic: GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
EST: gi|211147087|gb|FL480722.1|FL480722
EST:     GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAG                         CTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
genomic: GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
EST: gi|13382160|gb|BG458835.1|BG458835
EST:     GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAG                         CTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
genomic: GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
EST: gi|8383114|gb|BE055997.1|BE055997
EST:     GAATGACCTCTCTTCCAGAATTTCTTCCAGTTCTTCCTGTCATTCCTGAG                         CTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
genomic: GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
EST: gi|6020457|gb|AW065385.1|AW065385
EST:     GAATGACCTCTCTGCCAGAATT-CTTCCAGTTCTTTCTGTCATTCCTGAG                         CTTCCACCGGAG-CCCAAC
genomic: GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAAC
EST: gi|5762187|gb|AI967235.1|AI967235
EST:     GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAG                         CTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
genomic: GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
EST: gi|71768064|gb|DR966001.1|DR966001
EST:     GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAG                         CTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC
genomic: GAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACC

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: 45 (upstream exon), 43 (downstream exon)
Score: 29

CATAGAGAAGGAAGGTGGTAGCACGGATGAACTTGCTCTTGCGCTGTATGGAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACCAATCGTATTTTATCTCGGGCTCTCGCGAGAACCATTAGAAGACTCATGT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 14

CATAGAGAAGGAAGGTGGTAGCACGGATGAACTTGCTCTTGCGCTGTATGGAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACCAATCGTATTTTATCTCGGGCTCTCGCGAGAACCATTAGAAGACTCATGT


Block sizes: 44 (upstream exon), 29 (downstream exon)
Score: 2

CATAGAGAAGGAAGGTGGTAGCACGGATGAACTTGCTCTTGCGCTGTATGGAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACCAATCGTATTTTATCTCGGGCTCTCGCGAGAACCATTAGAAGACTCATGT


Block sizes: 44 (upstream exon), 40 (downstream exon)
Score: 9

CATAGAGAAGGAAGGTGGTAGCACGGATGAACTTGCTCTTGCGCTGTATGGAATGACCTCTCTGCCAGAATTTCTTCCAGTTCTTTCTGTCATTCCTGAGgtaagttgga ... tccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACCAATCGTATTTTATCTCGGGCTCTCGCGAGAACCATTAGAAGACTCATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcaaaatccacatggcacatggctcatttgtgtatacccttctccatcgaagCTTCCACCGGAGTCCCAACAGCAGTTGCTTCTTCTGCCAGCGGATTTAACCAATCGTATTTTATCTCGGGCTCTCGCGAGAACCATTAGAAGACTCATGT
                                     tacccttctccatc  CT-rich tract
     aaaat  TA-rich tract