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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGgtaagagtaacaatttgctaatttctattcactgaagcactgtcctaactgattttggcatttgtacctgcag

Basic information

species Zea mays
transcript GRMZM2G409430_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409430_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g54240.2 (Oryza sativa), 5'ss of exon 9
GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGgtaagagtaacaatttgc----taatttctatt-----cactgaagcactg--tcctaactgattttggcatttgtacctgcag
||||||||||| |||||||||||||||||||| |||||||||||   |   || ||    | |||| |  |     |  |||| || ||  || |||    ||||| ||||||||  |||||
GTTGTCTTGGCTGAATGCACAAAAAATTTTGGTCCTTGgtaagatgtattgttggccatttgatttatgctgccaactttgaaacattgcatcttaatgtgttttgccatttgtaaatgcag
















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|31358807|gb|CD443164.1|CD443164
EST:     GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTG                         GCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGA
genomic: GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGgtaagagtaa ... gtacctgcagGCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGA
EST: gi|7216514|gb|AW562636.1|AW562636
EST:     GAGGTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTG                         GCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGA
genomic: GAGGTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGgtaagagtaa ... gtacctgcagGCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGA
EST: gi|211161262|gb|FL391022.1|FL391022
EST:     GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCSCTTG                         GCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGA
genomic: GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGgtaagagtaa ... gtacctgcagGCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGA

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: 38 (upstream exon), 49 (downstream exon)
Score: 135

GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGgtaagagtaa ... gtacctgcagGCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGATATTATGTTGCATGAAGAGCGACCTAACTTAGGCGGTATAAGCATAGAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 28

GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGgtaagagtaa ... gtacctgcagGCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGATATTATGTTGCATGAAGAGCGACCTAACTTAGGCGGTATAAGCATAGAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 40

GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGgtaagagtaa ... gtacctgcagGCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGATATTATGTTGCATGAAGAGCGACCTAACTTAGGCGGTATAAGCATAGAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 22

GTTGTCTTGGCAGAATGCACAAAAAATTTTGGCCCTTGgtaagagtaa ... gtacctgcagGCTGGTCACACATGCTATGGAACTTCTGACAGCTGATAATGACTATGCGGATATTATGTTGCATGAAGAGCGACCTAACTTAGGCGGTATAAGCATAGAG