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

gtaagaaataaaaaaaatgcacatctgattcattctaatcacctgcataaataaaatttgcactaatatgtactcccaacgcattttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG

Basic information

species Zea mays
transcript GRMZM2G066578_T01
intron # 6
splice site 3'
intron type U2

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|76018387|gb|DT945557.1|DT945557
EST:     CCAAAGTTGCTCGTGCTGTTCCCGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
EST: gi|12058339|gb|BF729405.2|BF729405
EST:     CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
EST: gi|211441119|gb|FL034998.1|FL034998
EST:     CCAAAGTTGCTCGTGCTGTTGCTGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTATCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
EST: gi|8577333|gb|BE129970.1|BE129970
EST:     CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
EST: gi|78091932|gb|DV520306.1|DV520306
EST:     CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
EST: gi|7844522|gb|AW787744.1|AW787744
EST:     CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
EST: gi|211355369|gb|FL034995.1|FL034995
EST:     CCAAAGTTGCTCGTGCTGTTGCTGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTATCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
EST: gi|211355368|gb|FL034994.1|FL034994
EST:     CCAAAGTTGCTCGTGCTGTTGCTGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTATCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
EST: gi|211355370|gb|FL034996.1|FL034996
EST:     CCAAAGTTGCTCGTGCTGTTGCTGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTATCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
EST: gi|211441121|gb|FL035000.1|FL035000
EST:     CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCA-CAAGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCA
EST: gi|89757800|gb|DY687246.1|DY687246
EST:     GTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTACCATTTTTCTTAAGCCTAACATGGC
genomic: GTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCA-TTTTCTTAAGCCTAACATGGC
EST: gi|78179861|gb|DV550234.1|DV550234
EST:     CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAG                         GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA
genomic: CCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 76

GAATAGTGTTCCTCAAGGCACAGATCAAGTTGTTCTCGCAGGGAATATTTCCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG


Block sizes: 32 (upstream exon), 46 (downstream exon)
Score: 3

GAATAGTGTTCCTCAAGGCACAGATCAAGTTGTTCTCGCAGGGAATATTTCCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1711

GAATAGTGTTCCTCAAGGCACAGATCAAGTTGTTCTCGCAGGGAATATTTCCAAAGTTGCTCGTGCTGTTGCCGCAGCATTGTGTAGGAAGAATATCAAGgtaagaaata ... ttttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacctgcataaataaaatttgcactaatatgtactcccaacgcattttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG
                      cactaat  putative branch site (score: 1711)
                                             ttttgctc  putative PPT
        ataaataaaatttgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaataaaaaaaatgcacatctgattcattctaatcacctgcataaataaaatttgcactaatatgtactcccaacgcattttgctcagGTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG