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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagcaaaactctttctacaggttttctcttctagcaacttagagactaagtccaacttcaaaatacag

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 5'ss of exon 13
ACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagcaaaactctttctacaggttttctcttctagcaacttagagactaagtccaacttcaaaatacag
|| || |||||||| |||||||||||||| ||||| |||||||||||||||||||||||||| || || ||| ||||||||||||||||||| ||||||||| |||  | ||||| | ||| |  |   |    |    | ||||||||| |  |||||| || | |||
ACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAGgtatgacgcattattctttgtccagctcattgat----gtgcttcagagactaaata-aacttccaattgcag

upper sequence: GRMZM2G075978_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 5'ss of exon 12
ACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatg-aagcaaa---actctttctacaggttttctcttctagcaacttagagactaagtccaacttcaaaatacag----------------------------------------------------------------------------
|| || || || ||||| ||||||||||| || |||||||||||||||||||| ||||| || |||||||| ||||| | ||||   ||||| |||||| | ||| |||   ||  ||  | |||   || | |    | |  | | ||   ||    |  || |  ||  ||                                                                            
ACTGCTCAGGACAATATCGATCTGCAGACAACAATTCTTTCTAGATTTGATCTTATCTTCATTGTCAAGGACATCAGGAAGTATTCCCAAGACAAGgtaagcaaggaaaggaacaattctttcagaaattttat----gtagttaaaagggaaaacagagattaatgatggaggtcactgttattggaaagtttgcttcgttgcttgcttattatgtagacatgattaatgtttataatcttttcacag
















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|32824593|gb|CD964315.1|CD964315
EST:     TTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG                         AGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCA
genomic: TTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagca ... caaaatacagAGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCA
EST: gi|32939404|gb|CF044223.1|CF044223
EST:     TTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG                         AGAATAGCAAGCCACATTATCAAGGTGCATGCCATTGGTGCCGCAGCTTCA
genomic: TTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagca ... caaaatacagAGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCA
EST: gi|32833256|gb|CD972934.1|CD972934
EST:     TTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG                         AGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCA
genomic: TTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagca ... caaaatacagAGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCA
EST: gi|76933305|gb|DV173408.1|DV173408
EST:     GTATGATCAAGATAAG                         AGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCA
genomic: GTATGATCAAGATAAGgtatgaagca ... caaaatacagAGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCA
EST: gi|22546223|gb|BU098534.1|BU098534
EST:     TTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG                         AGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCA
genomic: TTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagca ... caaaatacagAGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 175

ACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagca ... caaaatacagAGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCATCCACAAACACAGAGGGGAGTGAAGGAGAGAATTGGCTGAAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 46

ACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagca ... caaaatacagAGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCATCCACAAACACAGAGGGGAGTGAAGGAGAGAATTGGCTGAAAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 15

ACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagca ... caaaatacagAGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCATCCACAAACACAGAGGGGAGTGAAGGAGAGAATTGGCTGAAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 7

ACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAGgtatgaagca ... caaaatacagAGAATAGCAAGCCACATTATCAAGGTGCATGCCAGTGGTGCTGCAGCTTCATCCACAAACACAGAGGGGAGTGAAGGAGAGAATTGGCTGAAAAG