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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACAATGACAAGGAACGAGCCCGAGATCGAGGCCTTGAGCCCAACGGGTTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacagtctctcacacagagctagctagactgcccgcttcactactgaacgtaccctagcctgcaactcttactcgtcgtgctgttctttcccgtgttctattttcccttttatttttccag

Basic information

species Zea mays
transcript GRMZM2G141399_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141399_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os08g09230.2 (Oryza sativa), 5'ss of exon 15
TGGACAATGACAAGGAACGAGCCCGAGATCGAGGCCTTGAGCCCAACGGGTTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacagtctctcacacagagctagctagactgcccgcttcactactgaacgtaccctagc----ctgcaactcttactcgtcgtgctgttctttcccgtgttctattttcccttttatttttccag
| ||| ||||||| || || || |||| || ||||||||| || || ||||| |||||||| ||||||||  | || ||||| || ||||| ||||||||||||| ||     | |||       | |   || ||| |  || |   |||||| ||  |   |    |  | |  |  | || || ||     | | |  ||| |                        
TAGACCATGACAAAGACCGGGCTCGAGTTCTAGGCCTTGAACCAAATGGGTTCAGCTTTGATGGAGCTGACTGTAATGGTGTGGATTACGCCCTGAACAGgcaagtac--ctccacacctcacaattgtgtgaatgcacaattga--gctgaacataatcgtacagaaccccgagccaaattcatcatgtga--catccgtgtggt------------------------

upper sequence: GRMZM2G141399_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os08g09230.1 (Oryza sativa), 5'ss of exon 15
TGGACAATGACAAGGAACGAGCCCGAGATCGAGGCCTTGAGCCCAACGGGTTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacagtctctcacacagagctagctagactgcccgcttcactactgaacgtaccctagc----ctgcaactcttactcgtcgtgctgttctttcccgtgttctattttcccttttatttttccag
    | ||||||| || || || |||| || ||||||||| || || ||||| |||||||| ||||||||  | || ||||| || ||||| ||||||||||||| ||     | |||       | |   || ||| |  || |   |||||| ||  |   |    |  | |  |  | || || ||     | | |  ||| | | |                    
----CCATGACAAAGACCGGGCTCGAGTTCTAGGCCTTGAACCAAATGGGTTCAGCTTTGATGGAGCTGACTGTAATGGTGTGGATTACGCCCTGAACAGGCAAgtac--ctccacacctcacaattgtgtgaatgcacaattga--gctgaacataatcgtacagaaccccgagccaaattcatcatgtga--catccgtgtggtttgt--------------------
















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|67021517|gb|CO450266.1|CO450266
EST:     TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAG                         GGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTNTGCA
genomic: TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTT-TGCA
EST: gi|31352858|gb|CD437215.1|CD437215
EST:     TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAG                         GGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
genomic: TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
EST: gi|32835013|gb|CD974691.1|CD974691
EST:     TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTATGCCCTGAACAG                         GGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTGCCTCTGCAA
genomic: TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
EST: gi|13149461|gb|BG319783.1|BG319783
EST:     TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAG                         GGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
genomic: TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
EST: gi|24768255|gb|CA403384.1|CA403384
EST:     TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAG                         GGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
genomic: TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
EST: gi|67014870|gb|CO443619.1|CO443619
EST:     TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAG                         GGCGATCTCAGCTTGGTTCGATGCCCCGGAGCTG-TTCCA
genomic: TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCC-GGAGCTGGTTCCA
EST: gi|24764332|gb|CA399497.1|CA399497
EST:     TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAG                         GGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
genomic: TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
EST: gi|31351712|gb|CD436069.1|CD436069
EST:     TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAG                         GGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA
genomic: TTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAA

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: 45 (upstream exon), 45 (downstream exon)
Score: 59

TGGACAATGACAAGGAACGAGCCCGAGATCGAGGCCTTGAGCCCAACGGGTTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAAGAGAGTCATGGAGCAGGACTGGTCGTGGAACCGACCTGCCCTCGACTAC


Block sizes: 28 (upstream exon), 44 (downstream exon)
Score: 7

TGGACAATGACAAGGAACGAGCCCGAGATCGAGGCCTTGAGCCCAACGGGTTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAAGAGAGTCATGGAGCAGGACTGGTCGTGGAACCGACCTGCCCTCGACTAC


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 4

TGGACAATGACAAGGAACGAGCCCGAGATCGAGGCCTTGAGCCCAACGGGTTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAAGAGAGTCATGGAGCAGGACTGGTCGTGGAACCGACCTGCCCTCGACTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 50

TGGACAATGACAAGGAACGAGCCCGAGATCGAGGCCTTGAGCCCAACGGGTTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacag ... atttttccagGGCGATCTCAGCTTGGTTCGATGCCCGGAGCTGGTTCCACTCCCTTTGCAAGAGAGTCATGGAGCAGGACTGGTCGTGGAACCGACCTGCCCTCGACTAC


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGACAATGACAAGGAACGAGCCCGAGATCGAGGCCTTGAGCCCAACGGGTTTAGCTTTGACGGAGCTGATAGCAACGGTGTTGACTACGCGCTGAACAGgcaagcacagtctctcacacagagctagctagactgcccgcttcactactgaacgtaccctagcctgcaactcttactcgtcgtgctgttctttcccgtgttctattttcccttttatttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT