Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactcactacagtactcagtttctcttgctcgatctgtataccagctagccatcactagacttgggaataatataatgtggcatgcatgcag

Basic information

species Zea mays
transcript GRMZM2G042364_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042364_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g58910.1 (Oryza sativa), 5'ss of exon 1
AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactcactacagtactcagtttctcttgctcgatctgtataccagctagccat-cactagacttgggaataatat-aatgtggcatgcatgcag-------
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| |||| || ||||| || || ||| |||| |||||||| || |  |     | | ||  ||  |  |  | || | |  |  | ||     | || |  |  ||   ||  | |   |||   ||  ||| |        
AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTCGCCACCATCTCCATCGCACCCTTCGCCCTCCTCCTCGAGAGgtaataatttc----atgcacaaattaacg-gagcaatat-tgcagtaactgatgttgcattgtaactgacgatggtgttggtgtttgatcaatggaaatggcag

upper sequence: GRMZM2G042364_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA15G36200.1 (Glycine max), 5'ss of exon 1
AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtac-tactcactaca---gtactcagtttctcttgctcgatctgtataccagctagccatcactagacttgggaataatataatgtggcatgcatgcag--------
|||| || |||||||| |||||||||||||| || || || ||||| |||||||| ||||||||||     || || || |||||  | ||  |||| ||||   ||   | || |     || |   |    |  |    ||  | ||| || |     |||  |  ||| | ||    ||  |    |||   | ||         
AGGTTTCTCTCAACCAAGGCATGAGCCACTATGTCCTTGTGGTCTATCGCCACGCTTTTGCCACCGCTGTCATAGCTCCTTTTGCCATTATTTTTGAAAGgtttatataaaataaacataaaccctagtgtcatcaccttgtcattttactagttt-ttgtcataaagctttgcaaattaatgcttactcattgtttcaattttccag

upper sequence: GRMZM2G042364_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G25890.1 (Glycine max), 5'ss of exon 1
AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtact---actcactacagtactcagtttctcttgctcgatctgtataccagctagccatcactagacttgggaataatataatgtggcatgcatgcag----------------
|||| ||||||||||| |||||||||||||| || || || || || |||||||| ||||||||||     || || || |||||  | ||  |||| |||| |    | | |  | |   || ||| ||     || | ||  | |||   ||     |      |||    |    |  ||  |       |  ||                 
AGGTTTCCCTCAACCAAGGCATGAGCCACTATGTCCTTGTGGTTTATCGCCACGCTTTTGCCACCGCTGTCATCGCTCCTTTTGCCTTTATTTTTGAAAGgttcatagaataaacataaaccttagtgtcatcatcttg-tcattttactctctcttttttttgttactataaagctttgcaaattaatgcttactcattgtttcaattttccag

upper sequence: GRMZM2G042364_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT5G07050.1 (Arabidopsis thaliana), 5'ss of exon 1
AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactcactacagtactcagtttctcttgctcgatctgtataccagctagccatcactagacttgggaataatataatgtggcatgcatgcag--------
|  | |||||||||  ||| ||||||||||| || || |||||||||||||| ||  ||||||||| |  ||||||||| |||||| || || | || ||||  ||  || |  | || |    ||   ||  | ||  | ||| |  || |   |||  |||| |||  |||    |       | |  || | |        
AAATATCCCTCAACACCGGTATGAGCCACTATGTCCTTGTCGTCTACCGCCATGCAATTGCCACCGCCGTTATTGCACCCTTTGCTTTCTTCTTCGAAAGgttatatccatttaattattttcattacattctttgaattttattc--gccaataatcgataga-ttgttaatggattctaactacgtatattccgttttacag

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|5740584|gb|AI948274.1|AI948274
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAG                         GAAGGGGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
EST: gi|211124594|gb|FL137144.1|FL137144
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTG-TCTCATCCTTGAGAG                         GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
EST: gi|50335600|gb|CO530726.1|CO530726
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAG                         GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
EST: gi|211123823|gb|FL137137.1|FL137137
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAG                         GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
EST: gi|149099820|gb|EE185873.2|EE185873
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAG                         GAAGGTGAGGCCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTTCGTG
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCC-AACATGACGTGGTCCGTCTTCCTCCAGATCTT-CGTG
EST: gi|211123824|gb|FL137138.1|FL137138
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAG                         GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
EST: gi|211123825|gb|FL137139.1|FL137139
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAG                         GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
EST: gi|211123828|gb|FL137142.1|FL137142
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAG                         GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
EST: gi|78023216|gb|DV491603.1|DV491603
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAG                         GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
EST: gi|211124593|gb|FL137143.1|FL137143
EST:     CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAG                         GAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT
genomic: CACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTT

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: 41 (upstream exon), 17 (downstream exon)
Score: 4

AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 36

AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 245

AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 25

AGGTCTCCCTCAACCACGGCATGAGCCACTACGTGCTCGTCGTCTACCGCCACGCCTTTGCCACCGTCTCTATTGCACCGTTTGCTCTCATCCTTGAGAGgtactactca ... atgcatgcagGAAGGTGAGGCCCAACATGACGTGGTCCGTCTTCCTCCAGATCTTCGTGTTGGCACTGCTCGG