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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtacatttatttccctaatttattcatgttcactgcttacataatctagcttatgcttccaagtgtaatttgcatgtagcatgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG

Basic information

species Zea mays
transcript GRMZM2G389362_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 5
gttggtacatttatttccctaa-tttattcatgttcactgcttacataatctagcttatgcttccaagtgtaatttgcatgtagcatgctcttaatattcatt--------ttattttgatct-tagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
|||||| |||| |||||  ||  ||| |   ||||  ||  || ||| ||  |  ||       ||||  ||| |||| ||   | |||| ||| ||||  ||        ||| || ||  | ||||||||||||||||||||||| | |||||||||||||||||||||||||| ||||||||||||||| |||||||||||
gttggtgcattaatttcaataggtttctatctgtttgctcatt-catgataaaaatttatacagcaagcttaacttgcttgggccttgcttttagtatttgttcattcatgttacttcgaattgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG

upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 5
gttggtacatttatttcccta-atttattcatgttcactgcttacataatctagcttatgcttccaagtgtaatttgcatgtagcatgctcttaatattcatt---------------ttattttgatct-tagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
|||||| |||| |||||  || |||| |   ||||  ||  || ||| ||  |  ||       ||||  ||| |||| ||   | |||| ||| ||||  ||               ||| || || || ||||||||||||||||||||||| | |||||||||||||||||||||||||| ||||||||||||||| |||||||||||
gttggtgcattaatttcaatagatttttatctgtttgctcatt-catgataaaaatttatacagcaagcttaacttgcttgggccttgcttttagtatttgttcattcatgattcatgttacttcgaactgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG

upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
gttggtacatttatttccctaatttattcatgttcactgcttacataatctagcttatgct-tccaagtgtaatttgcatgtagca--tgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
                    ||   | |||| ||  |  ||  ||   | ||   |  | | ||      || |||| ||  |  |  || | | |     ||||   | ||  |   ||| ||  |||||||||||||| |  | ||||||||||| |||||||| || || ||||||||||| |||||||||| |
-------------------caagcaactcatcttt-cacctggcaatgtgtaatgtgcgttatcttcccttattttggataaaagaattgatatcaggtaccattgattattctttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG

upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 5
gttggtacatttatttccctaatttattcatgttcactgcttacataatctagcttatgcttccaagtg-taatttgcatgtagca--tgctcttaatattcatt--ttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
                    ||| | |  || | ||||  |  ||   | ||   | || |  ||  || || |||| ||  |  |  || | | |     ||||  |||| ||  |   ||| ||  |||||||||||||  |  | ||||||||||| |||||||| || || ||| ||||||| |||||||||| |
-------------------caatct-tatatctccact--tggcaatgtgtaatgtgtgttgtcatttgctattttggataaaagaattgatatcaggtaccattgattatattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG

upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G41070.3 (Glycine max), 3'ss of exon 5
gttggtacatttatttccctaatttattcatgttcactgcttacataatc-tagcttatgcttccaagtgtaatttgcatgtagcatgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
                   | || ||   |   ||| |       || |  ||||| |  | |  || |  ||| |   |  || | |||  | || || | |   | ||  |   |||  |  |||||||||||||  | || ||||||||||| |||||||| || ||  || ||||||| |||||||||| |
--------------gattttgatctagataaaatca-tataggtgtactggtagctgactcattgaaattgaatct-tgttcag-aagctaatgat-tttactgattattctttgcagACCTGGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAGG

upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 5
gttggtacatttatttccctaat-ttattcatgttcactgcttacataatctagcttatgcttccaagtgtaatttgcatgtagcatgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
    | |  || || |   |||  ||||  | ||  ||||        | ||  || |   ||  || || |  ||      |   |  |  |  || | ||| |  ||||     |||  |  |||||||||||||  | || ||||||||||| |||||||| || ||  || ||||||| ||||||||||  
----ggattttgatctagataaaattatataggtgtactggc------agctgactca---ttgaaattgaatctttttcagaagctaatggttttactgattattctttg----caGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG-

upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
gttggtacatttatttccctaatttattcatgttcactgcttacataatctagcttatgcttccaagtgtaatttgcatgtagcatgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
     || |||   ||   ||    ||  ||  |      | |   ||   ||  ||  |  ||  ||| |||  | ||  | | |  |||     || | | |  | |      |||  || | |||||||||||  | || || |||||||| || ||||| |||||||||||||| || ||||||||||||
-----tatattatattatttaggaaataaattgtggt--atgaagcaaatgag--tacacacccttgtggaatcagtattcatcttcttct----gttaactgttctcta----cagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG

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|67022369|gb|CO451118.1|CO451118
EST:     TTGTGCTTGTTTTAAGGAA-CTACTGAGCCAGCCGTTTGCTTGAGTGAAG                         ATATACAAACAA
genomic: TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAA
EST: gi|211315830|gb|FK969313.1|FK969313
EST:     TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG                         ATATACAAACAAATGAGTGCCTAGAGA
genomic: TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGA
EST: gi|211313814|gb|FK969304.1|FK969304
EST:     TTGTS-TGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG                         ATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|211313815|gb|FK969305.1|FK969305
EST:     TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG                         ATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|32937726|gb|CF042545.1|CF042545
EST:     TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG                         ATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|211313813|gb|FK969303.1|FK969303
EST:     TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG                         ATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|67026759|gb|CO455508.1|CO455508
EST:     TTGTGCTGGTTTTAAGGATACTACTGAGCCAGCCGTTTGCTTGAGTGAAG                         ATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|32937931|gb|CF042750.1|CF042750
EST:     TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAG                         ATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: TTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA

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: 48 (upstream exon), 49 (downstream exon)
Score: 227

GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 166

GTAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGTTTTAAGGAAACTACTGAGCCAGCCGTTTGCTTGAGTGAAGgttggtacat ... ttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaagtgtaatttgcatgtagcatgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
                                      ttttatttt  CT-rich tract
                          tcttaatattcatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtacatttatttccctaatttattcatgttcactgcttacataatctagcttatgcttccaagtgtaatttgcatgtagcatgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT