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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaaagtgtgccttactgtcatctcatttatcttcctccatcacactttgccttactgacgcttcaagttcaaactaatatgacctatctacttcaaaag

Basic information

species Zea mays
transcript GRMZM2G174730_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 5'ss of exon 6
GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaaagtgtgccttactgtcatctcatttatcttcctccatcacactttgccttactgacgcttcaagttcaaactaatatgacctatctacttcaaaag
|||||  ||| || || ||||||||| |||||||||| ||||| |||||| | ||||||||||||| | ||||||||| ||  || |||    ||||           || | |   ||    |   | | |   | |  ||||||||| |   | | | |||  | ||
GATTGGCAGCCTGCCTATTTTGGAATATCATAGCAACCACAACCGCATGGGTAAAAGGGGAAGgtaaagctaaagtgtacccaaccgtc--tacattg---------tatgaaa---tgtgccatgaatgttgacactcaaaactaataggtgttctgtgctttgacag

upper sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 5'ss of exon 7
GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgt-ataactaaagtgtgccttactgtcatctcatttatcttcctccatcacactttgccttactgacgcttca-agttcaaactaatatgacctatctacttcaaaag
|||||  |   || ||    |||||| | ||||||||||| |||||||||||||||||||||||| |  |      |||| |||  ||  || |  ||||| ||  |  ||  ||  ||   |  || || |   | |  |  | || ||||    | || | || |    
GATTGGCATGCTGCCTTACATGGAATATTATAGCAACTACTACAGCATGGATTAAAGGGGAAGgtcagtatctgcttgtgtctt--tgg-atttgctttatatttttgtat-gcagatttgatggctaacacagtacaacttgatcttatat--tttttccaatttag---
















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|149076952|gb|EE165608.2|EE165608
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|211455821|gb|FL370764.1|FL370764
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCMTGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTTGCTTGCCATTATCTACTTCATATCTGGTGCGC
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCT-GCTTGCCATTATCTACTTCATATCTGGTGCGC
EST: gi|31353834|gb|CD438191.1|CD438191
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|211137749|gb|FL292364.1|FL292364
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTAT
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTAT
EST: gi|71322126|gb|DR797758.1|DR797758
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|211198979|gb|FL379473.1|FL379473
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|37400724|gb|CF637721.1|CF637721
EST:     TCTCTTTT-GAATGTCATAGCAACTAC-ACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|149069546|gb|EE157919.2|EE157919
EST:     TCTCTTTTGGAATGTCATAGCAACTACCACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|76927277|gb|DV171213.1|DV171213
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|4152018|gb|AI372152.1|AI372152
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACACCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|5847119|gb|AW000198.1|AW000198
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|76289053|gb|DV028621.1|DV028621
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|149079646|gb|EE168643.2|EE168643
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|78081465|gb|DV509877.1|DV509877
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|32938227|gb|CF043046.1|CF043046
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCACGGATTAAAGGGGAAG                         GTGTTATGATCTGG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGG
EST: gi|76289052|gb|DV028620.1|DV028620
EST:     GGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: GGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|5343187|gb|AI795372.1|AI795372
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|78112246|gb|DV530640.1|DV530640
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
EST: gi|149104177|gb|EE289611.2|EE289611
EST:     TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG                         GTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG
genomic: TCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTG

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: 364

GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTGGGGCTTATGTGTTATGGTATCGACCTCTTTATAATGCAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTGGGGCTTATGTGTTATGGTATCGACCTCTTTATAATGCAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTGGGGCTTATGTGTTATGGTATCGACCTCTTTATAATGCAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 412

GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaa ... acttcaaaagGTGTTATGATCTGGCTGCTTGCCATTATCTACTTCATATCTGGTGCGCCTGGGGCTTATGTGTTATGGTATCGACCTCTTTATAATGCAATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAGgtataactaaagtgtgccttactgtcatctcatttatcttcctccatcacactttgccttactgacgcttcaagttcaaactaatatgacctatctacttcaaaag

- - - - - - - - - - - - - - - - - - - - - -  CATGGA