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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaaggatggccactgaagttgtataataagttgtaacagacaagcactggcctttgggcaaaattttgcag

Basic information

species Zea mays
transcript GRMZM2G064212_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g58560.1 (Oryza sativa), 5'ss of exon 3
GCTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaaggatggccactgaagttgtataataagttgtaacagacaagcactggcctttgggcaaaattttgcag
|||||||||| || ||||||||||||   |||||||||||||||||||| |||||||| |||||||| || |||||||||||||||||       | |  | |   | ||       |           |  |||||| | ||||| |||    |   |  ||      | |                      
GCTTTGATGCCATCTCTGATTCCAAGTATACTAGTGATGTGAACTGGGGCTGCATGGTCAGAAGCAGCCAGATGCTGGTTGCTCAGgtgcttgtcgactttatttgattgaaataacagcatttttt--ttaccactgcatttgtaaaatgtacttggatggatttttgcag----------------------

upper sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g27350.3 (Oryza sativa), 5'ss of exon 4
GCTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaaggatggccactgaagttgtataataagttgtaacagacaagcactggcctttgggcaaaattttgcag
|||||||||| || |||||||||||    ||||||||||| |||||||| || ||||| |||||||| ||||||||||||||||||||     |  |||||   | |       || |||||  |||     |  ||    ||        || |||||   | ||  | |||  |||||    | ||||||||
GCTTTGATGCCATCTCTGATTCCAAATATACTAGTGATGTCAACTGGGGCTGTATGGTCAGAAGCAGCCAAATGCTGGTTGCTCAGgt-----ccttccctactata------tttaattga--aagcgcttctcctttttttaccactgcagatgtaa---ataa--aatggtatttggatggatttttgcag

upper sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G48380.1 (Glycine max), 5'ss of exon 3
GCTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaagg------atggccactgaagttgtataataag--ttgtaacagacaagcactggcctttgggcaaaattttgcag--------------------
|||||||||| ||    ||| | |||   || |||||||| || ||||| || ||| || |||||||||| ||||||||||||||||||   |   | |  |  || |  | | |||    |  ||        |||    || |  || | |  |     || |  |          || | ||      |||  |   |                     
GCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAGgtatgatgccttctatataatgattgcttttgacaaggaaattgttacatgataccttatattttctgtttttcttttttgcctgtttttgttgtctttcaaaataaagctactaatgtggcttccttgtgcacag

upper sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv00s0215g00030.t01 (Vitis vinifera), 5'ss of exon 4
GCTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaaggatggccactgaagttgtataataagttgtaacagacaagcactggcctttgggcaaaattttgcag
| ||||| || ||    ||||| ||| |||||||||||||||| ||||| |||||| || |||| ||||| ||||| ||||| |||||    |       | |   | |||   || |||    |  ||       |   |    |   |   |  |    |  |     |||   ||    |||||       
GTTTTGAGGCTATTGGGGATTCAAAGTTAACTAGTGATGTGAATTGGGGTTGCATGCTTCGAAGTAGTCAGATGCTTGTTGCACAGgtgtggtgctcttttgtttcactgttatttaattagtaagagacatatttttttggcacactttctataatttttg-tacaatttggaagttacttaaaat-------

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|91050792|gb|EB161210.1|EB161210
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
EST: gi|148950021|gb|EC895550.2|EC895550
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
EST: gi|93284688|gb|EB676952.1|EB676952
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAA-CCCCCAGAGAAG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
EST: gi|60341279|gb|DN208252.1|DN208252
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
EST: gi|22490393|gb|BU050316.1|BU050316
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTC-CCACCTTGGAAGATCTTGG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGG
EST: gi|20300180|gb|BQ163123.1|BQ163123
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACC-CCTAGGAAGATCTTGG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGG
EST: gi|76926912|gb|DV171049.1|DV171049
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
EST: gi|19057951|gb|BM736618.1|BM736618
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCT-GGAAGATCT
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCT
EST: gi|71320082|gb|DR796796.1|DR796796
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
EST: gi|211065965|gb|FK946610.1|FK946610
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
EST: gi|87153634|gb|DY398423.1|DY398423
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGG
EST: gi|148958416|gb|EC904649.2|EC904649
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
EST: gi|148965028|gb|EE015858.2|EE015858
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAG
EST: gi|14244146|gb|BG842173.2|BG842173
EST:     ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG                         GCGCTGATTTTTCA
genomic: ATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctg ... aattttgcagGCGCTGATTTTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAGgtaaactctgtccctttcaaagtgtccctttattgaccaaggatggccactgaagttgtataataagttgtaacagacaagcactggcctttgggcaaaattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG