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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCCTAATTACATACGTTGCCTTGAACCTTATGGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatgcctgcccctgacgatagtatctatctatgtatgtaggagtatttcatgccatgtcttctggataggttcctgtttttttgttttgttctattgttttgtttgttttaacaaaataccaaatttgtgcag

Basic information

species Zea mays
transcript GRMZM2G096343_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 13
GTCTCCTAATTACATACGTTGCCTTGAACCTTATGGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatgcctgcccctgacgatagtatctatctatgtatgtaggagtatttcatgccatgtcttctggataggttcctgtttttttgttttgttctattgttttgtttgttttaacaaaataccaaatttgtgcag
||||  | || || || ||||||||||||||||||||||| ||||| || || ||||| |||||||| |||||||| ||  | ||||||| | ||||  || ||    | ||    |  |   ||  |    |  |||  |||  |   ||    |  |   | || |  |                                                    
GTCTTATGATCACGTATGTTGCCTTGAACCTTATGGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaagcct-tccttgtgcctggtgagaaggttcatagcttcaggggtttagtgctctcattttaacacggcaccatgctactgcag------------------------------------------------

upper sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv02s0025g03400.t01 (Vitis vinifera), 5'ss of exon 13
GTCTCCTAATTACATACGTTGCCTTGAACCTTATGGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatgcctgcccctgacgatagtatctatctatgtatgtaggagtatttcatgccatgtcttctggataggttcctgtttttttgttttgttctattgttttgtttgttttaacaaaataccaaatttgtgcag
|||| || || ||||| || ||  ||||| | |||||||| |||||||| ||||| ||||| ||||||||||| |||||| | ||||| |     ||| | | | |   |    | | |     ||  |   | |   |     |  ||||     ||| ||    |   ||       |  |   |                                    
GTCTTCTCATCACATATGTGGCACTGAACTTGATGGATGGGCATGGCCAACCGGCACTCCTATACATCGTGCCATTCACACTGGgtaatt---ctctgtcacaggcagcaaatgcaacccg---attgaactgcaaaaccgattacatcttgcaattagcttatcatgaattcacacactgatgcag------------------------------------
















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|24934365|gb|CA452583.1|CA452583
EST:     GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCG                         GCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
genomic: GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
EST: gi|76282121|gb|DV021689.1|DV021689
EST:     GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCG                         GCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
genomic: GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
EST: gi|67041082|gb|CO467337.1|CO467337
EST:     GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCG                         GCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
genomic: GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
EST: gi|37376705|gb|CF624906.1|CF624906
EST:     GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCG                         GCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
genomic: GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
EST: gi|16921787|gb|BM075300.1|BM075300
EST:     GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCG                         GCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
genomic: GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
EST: gi|71422113|gb|DR805618.1|DR805618
EST:     GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCG                         GCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
genomic: GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
EST: gi|18163279|gb|BM333118.1|BM333118
EST:     GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCG                         GCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA
genomic: GGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGA

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: 157

GTCTCCTAATTACATACGTTGCCTTGAACCTTATGGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGACAAAAGGACAGCCCGAGAGAGTGTGCACGCACATGCACCCATCCCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

GTCTCCTAATTACATACGTTGCCTTGAACCTTATGGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGACAAAAGGACAGCCCGAGAGAGTGTGCACGCACATGCACCCATCCCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

GTCTCCTAATTACATACGTTGCCTTGAACCTTATGGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGACAAAAGGACAGCCCGAGAGAGTGTGCACGCACATGCACCCATCCCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GTCTCCTAATTACATACGTTGCCTTGAACCTTATGGATGGCCATGGCCAGCCGGCTCTCCTTTACATCGTGCCTTTCACAATCGgtaagtgatg ... atttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGACAAAAGGACAGCCCGAGAGAGTGTGCACGCACATGCACCCATCCCCCAA