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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaatatgggtattcaacaatggtaattgttttcagatttgttaaatcttttatcaacacggggcttctaaactgatggaatttctctcttataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG

Basic information

species Zea mays
transcript GRMZM2G006130_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 9
ccaatatgggtattcaacaatggtaattgttttcagatttgttaaatctt--ttatcaacacggggcttctaaactgatggaatttctctcttataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG
                      |||||  ||  || |||| ||| |||||  |   ||   | |  || || || || |   |   |||| |||||  |||||||| ||||| |||||||||||||||||||  || ||||| ||||||||||| 
----------------------gtaataattgccatattttttatatctttatcgccacagctgacctccttaattgctactaaa-ctcttttatatatcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCAATTGCTCCTTTTGTAAAA

upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 9
ccaatatgggtattcaacaatggtaattgttttcagatttgttaaatctt--ttatcaacacggggcttctaaactgatggaatttctctcttataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG
                      |||||  ||  || |||| ||| |||||  | | ||   | |  || || ||  ||    |      |   |||  |||||||| ||||| |||||||||||||||||||  || ||||| ||||||||||| 
----------------------gtaataattgccatattttttatatcttgatcaccacagctgacctcctgaatcgacactaaactctttaaata--tcagGAATCAGCCATAATGATGAAGTTGATACTGCTGCGATTGCTCCTTTTGTAAAA
















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|67030289|gb|CO459038.1|CO459038
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|32929408|gb|CF034220.1|CF034220
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|32923839|gb|CF028651.1|CF028651
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|32929966|gb|CF034778.1|CF034778
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|32924017|gb|CF028829.1|CF028829
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|32928349|gb|CF033161.1|CF033161
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTCGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|18654845|gb|BM499650.1|BM499650
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|211350725|gb|FL044598.1|FL044598
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCAC
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCAC
EST: gi|211221447|gb|FL389601.1|FL389601
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|32924613|gb|CF029425.1|CF029425
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|211079656|gb|FL402147.1|FL402147
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGNCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|32924051|gb|CF028863.1|CF028863
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|18963147|gb|BM660266.1|BM660266
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|211150003|gb|FL374637.1|FL374637
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|18661865|gb|BM501621.1|BM501621
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|21331549|gb|BQ486930.1|BQ486930
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGTCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|32924623|gb|CF029435.1|CF029435
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
EST: gi|32924183|gb|CF028995.1|CF028995
EST:     CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG                         GAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA
genomic: CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAA

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), 46 (downstream exon)
Score: 407

CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 1080

CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 704

CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 640

CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGgtaattgttt ... tataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttttatcaacacggggcttctaaactgatggaatttctctcttataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG
                                            ttataac  putative branch site (score: 640)
                                    tttctctcttat  CT-rich tract
                                          tcttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaatatgggtattcaacaatggtaattgttttcagatttgttaaatcttttatcaacacggggcttctaaactgatggaatttctctcttataactcagGAATAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG

- - - - - - - caacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgg