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'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATCTTTCATCAAATTTCATAAGTGGCTCTATTCCTATTGAGCTATCAAGGATCAACAATTTGGACACGTTgtaagccttcatcatctcacatgcattaatagtatccatttcgtgctaatcctatatataacatagatatatgtaccag

Basic information

species Zea mays
transcript GRMZM5G809695_T03
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G809695_T03 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 17
AAATCTTTCATCAAATTTCATAAGTGGCTCTATTCCTATTGAGCTATCAAGGATCAACAATTTGGACACGTTgtaagccttcatcatctcac--atgcatt-aatagtatccatttcgtgctaatcctatatataacatagatatatgtaccag
 ||| | |||||||||||  ||||||| |||||||||||||||||||| || ||||||||||||||||| ||||||| | |  |     ||   ||| |||  | | ||||  ||   | ||| |  | | | | |   || ||  |||| |||
GAATTTGTCATCAAATTTTCTAAGTGGTTCTATTCCTATTGAGCTATCGAGAATCAACAATTTGGACACCTTgtaagtcctgttagctccatctatgaattcgaaaatatctgttctatccta-ttgtgtgtgtgatg-aggtacctgtatcag
















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|31405872|gb|CD484604.1|CD484604
EST:     AGTGGCTCTATTCCTATTGAGCTATCAAGGATTAACAATTTGGACACGTT                         GGACTTATCCTGTAACATGATGACGGGTCCAATTCCATCATCCATTGGCAA
genomic: AGTGGCTCTATTCCTATTGAGCTATCAAGGATCAACAATTTGGACACGTTgtaagccttc ... tatgtaccagGGACTTATCCTGTAACATGATGACGGGTCCAATTCCATCATCCATTGGCAA
EST: gi|211505743|gb|FL354866.1|FL354866
EST:     AGTGGCTCTATTCCTATTGAGCTATCGAGGATCAACAATTTGGACACGTT                         GGACTTATCCTGTAACATGATGACGGGTCCAATTCCATCATCCATTGGCAA
genomic: AGTGGCTCTATTCCTATTGAGCTATCAAGGATCAACAATTTGGACACGTTgtaagccttc ... tatgtaccagGGACTTATCCTGTAACATGATGACGGGTCCAATTCCATCATCCATTGGCAA
EST: gi|32164946|gb|CD670264.1|CD670264
EST:     GGATCAACAATTTGGACACGTT                         GGACTTATCCTGTAACATGATGACGGGTCCAATTCCATCATCCATTGGCAA
genomic: GGATCAACAATTTGGACACGTTgtaagccttc ... tatgtaccagGGACTTATCCTGTAACATGATGACGGGTCCAATTCCATCATCCATTGGCAA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1938

AAATCTTTCATCAAATTTCATAAGTGGCTCTATTCCTATTGAGCTATCAAGGATCAACAATTTGGACACGTTgtaagccttc ... tatgtaccagGGACTTATCCTGTAACATGATGACGGGTCCAATTCCATCATCCATTGGCAACCTAGAGCATCTATTGAGGCT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 73

AAATCTTTCATCAAATTTCATAAGTGGCTCTATTCCTATTGAGCTATCAAGGATCAACAATTTGGACACGTTgtaagccttc ... tatgtaccagGGACTTATCCTGTAACATGATGACGGGTCCAATTCCATCATCCATTGGCAACCTAGAGCATCTATTGAGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

AAATCTTTCATCAAATTTCATAAGTGGCTCTATTCCTATTGAGCTATCAAGGATCAACAATTTGGACACGTTgtaagccttc ... tatgtaccagGGACTTATCCTGTAACATGATGACGGGTCCAATTCCATCATCCATTGGCAACCTAGAGCATCTATTGAGGCT