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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttcatatttttttgtttttccttgtatttgttgctagctaggggtaggaatatacattgaaatttggcaacttgcagtgttttataactactgaagtaactgggcttatgaatttcttatcttcattttcctgatacttttatactgagatttctattgcttcatgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG

Basic information

species Zea mays
transcript GRMZM5G813909_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 5
gtgtgttcatatttttttgtttttccttgta-tttgttgctagctaggggtaggaatatacattgaaatttggcaacttgcagtgttttataactactgaagtaactgggcttatgaatttcttatcttcattttcctgatacttttatactgagatttctattgcttcatgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG
         ||| ||| |||| |   || ||     |   |   ||   ||   || ||   |||||   ||   || ||||   ||    || |||  ||||| || |||||||||||||  ||| |||   | ||  | |  ||||| |||| |  ||||    |  |    ||  |||||||||| ||||||||||||||||| ||||||||||| ||||| ||||||||  || | || || || || ||||||||||| |||  ||||||||||
--------gtatgtttgtgttctcaattttagcacctcagttattatatgttttaacat---ttgaatggtgttcacctgcaagattagtgaagtacaaaagtatcttggcttatgaatttgctatgttctaatccccaacatatttattctga-acctctagctttggacttttttcagCAAACTATTTGGCTCTTCATTAGGGACATGATCAAAGGGATTTTGCTATCCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAG

upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgtgttcatatttttttgtttttccttgtatttgttgctagctaggggtaggaatatacattgaaatttggcaacttgcagtgttttataactactgaagtaactgggcttatgaatttcttatcttcattttcctgatacttttatactgagatttctattgcttcatgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG
                                                                                 || | |  ||  | |   | || ||     | |||    ||||  ||  |||  | || |  | |  | | |  || ||  |   |  ||  |   ||||||| |||||| | ||||||||||| |||||||||||||  || || ||  | ||| | || ||||| || || ||||| || || | |||||| |||
---------------------------------------------------------------------------------gtatgtcgtatttccaacactacct-----tgtga----cttacgtttttttatcagaga--tgtggattaaatttgcttctaaattctgt-tgacagCAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCTGTCATACTAGGCCCACCCATTGTTGCTGCGATAATTTTCATAGTCCAG
















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|211188255|gb|FL327236.1|FL327236
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAAGCTCGACATGNTTTTAACAAG                         CAAACTATATGGCTNCT-CATNAGGGGA-ATGATCAAAAGAATTTTACTAT
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCT-CTTCATTAGGG-ATATGATCAAAGGAATTTTACTAT
EST: gi|149101643|gb|EE187775.2|EE187775
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|71767568|gb|DR965505.1|DR965505
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|76293281|gb|DV032849.1|DV032849
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|71446633|gb|DR827683.1|DR827683
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|71330641|gb|DR802092.1|DR802092
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|211231531|gb|FL255915.1|FL255915
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|211231534|gb|FL255918.1|FL255918
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATCACCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|211231535|gb|FL255919.1|FL255919
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|6194775|gb|AW146879.1|AW146879
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|50322421|gb|CO517547.1|CO517547
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|211274143|gb|FL330839.1|FL330839
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGGATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|78114998|gb|DV533386.1|DV533386
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|78113447|gb|DV531839.1|DV531839
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|50334362|gb|CO529488.1|CO529488
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
EST: gi|71436743|gb|DR817793.1|DR817793
EST:     TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAG                         CAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC
genomic: TCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCC

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: 101

ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 54

ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 89

ATTACAGACTTGCCGTTCTCTCTCTATTCAACTTTTGTTATAGAGGCTCGACATGGTTTTAACAAGgtgtgttcat ... tgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcattttcctgatacttttatactgagatttctattgcttcatgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG
         tcctgat  putative branch site (score: 89)
              atacttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttcatatttttttgtttttccttgtatttgttgctagctaggggtaggaatatacattgaaatttggcaacttgcagtgttttataactactgaagtaactgggcttatgaatttcttatcttcattttcctgatacttttatactgagatttctattgcttcatgccttgtagCAAACTATATGGCTCTTCATTAGGGATATGATCAAAGGAATTTTACTATCCATGATATTGGGGCCACCAATCGTGGCTGCTATCATCTACATAGTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT