Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   
6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaaatcttcattcacatgttctgttcgtgtaattaatcatttcatcctgaggcagttggcatgacaagttacgttccattttgcag

Basic information

species Zea mays
transcript GRMZM5G804382_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 29
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaaatcttcattcacatgttctgttcgtgtaattaatcatttcatcctgaggcagttggcatgacaagttacgttccattttgcag-----
||||| |||||||| ||||| ||||||||||||| ||||| ||||||||||||| ||| | ||||||||||| || |||||||||||||||||||||||| |||| | | | | || || |||| || | | || | | || ||||||| ||| || |||| | |
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgta-------atctatagagattgctcttcttttggttattattc-tgttattatttagtaggcagcatgacgagtggtattacattgtatggtgcag

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 29
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaaatcttcattcacatgttctgttcgtgtaattaatcatttcatcctgaggcagttggcatgacaagttacgttccatt-ttgcag-------
||||| |||||||| ||||| ||||||||||||| ||||| ||||||||||||| ||| | ||||||||||| || |||||||||||||||||||||||| |||| | | | | || || |||| || | | || | | || ||||||| || || |||| ||| |
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgta-------atctatagagattgctcttcttttggttattattc-tgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcag

upper sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 29
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaaatcttcattca----catgttctgttcgtgtaattaatcattt--catcctgaggcagttggcatgacaagttacgttccattttgcag-------------------------------
|| ||| | || || ||||| | | ||||||| |||||| ||||||| || || | || ||||||||||| ||||| ||| || |||||||||||||||| | || || || | || | | | || | ||| | ||||| | |||| | | ||| | |||| ||
GTATACTGGTAAAGTTGATGAGCTTATCAAGGACAAAATTGAAGCACAGAAAGAGGAGAAAGCTAAAGAGAAGGAAGAGAAGGATGTTATTGCTCAGCAGgtacactccccccctcccccaatatcaaatgctttccat-tatgaagtcagataatatcctttttcttttgggtacatattttatctaatatttggctatcaaattaatactagtttcaattatctccag

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|211137943|gb|FL090180.1|FL090180
EST:     ATGAAGAAAGAGTCAAAGAGAAGGAGAAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|32827950|gb|CD967628.1|CD967628
EST:     GATCTCGTGGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: GATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|211434575|gb|FL418939.1|FL418939
EST:     ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|33093317|gb|CF053311.1|CF053311
EST:     ATGAAGAAAGAGTCAAAGAGAAGGAGAAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|32945927|gb|CF050746.1|CF050746
EST:     ATGAAGAAAGAGTCAAAGAGAAGGAGAAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|32794485|gb|CD946721.1|CD946721
EST:     GATCTTGTGGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: GATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|24934286|gb|CA452504.1|CA452504
EST:     ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|60355880|gb|DN222853.1|DN222853
EST:     ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|32826787|gb|CD966465.1|CD966465
EST:     GATCTCGTGGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: GATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|32846561|gb|CD986242.1|CD986242
EST:     ATGAAGAAAGAGTCAAAGAGAAGGAGAAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|32846264|gb|CD985945.1|CD985945
EST:     ATGAAGAAAGAGTCAAAGAGAAGGAGAAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
EST: gi|32847239|gb|CD986920.1|CD986920
EST:     ATGAAGAAAGAGTCAAAGAGAAGGAGAAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT
genomic: ATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCT

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: 98

ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCTGGCATGGGTGGCCCTCCACCTCCGATGGGTGGGATGGGCATGCCTCCAA


Block sizes: 49 (upstream exon), 16 (downstream exon)
Score: 53

ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCTGGCATGGGTGGCCCTCCACCTCCGATGGGTGGGATGGGCATGCCTCCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCTGGCATGGGTGGCCCTCCACCTCCGATGGGTGGGATGGGCATGCCTCCAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 61

ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaa ... cattttgcagAACATGTATGCGCAATTGCTTCCTCTTGCTTTGCCTGCTCCGCCAATGCCTGGCATGGGTGGCCCTCCACCTCCGATGGGTGGGATGGGCATGCCTCCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaaatcttcattcacatgttctgttcgtgtaattaatcatttcatcctgaggcagttggcatgacaagttacgttccattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA