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

TGAAAGATCCGTAGAATCGAGGGTGGTTACTTTGTTCAGGGAAAGACCATCAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccagatatttcatccttaaaatgaaattattcaattctagtgctgaacatgattctagtgctgaacatgcttctcaaacactgatggcactgcattaggatctgctaaatatataaaaacctctctatgtag

Basic information

species Zea mays
transcript GRMZM2G042099_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042099_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g54784.1 (Oryza sativa), 5'ss of exon 12
TGAAAGATCCGTAGAATCGAGGGTGGTTACTTTGTTCAGGGAAAGACCATCAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccagatatttcatccttaaaatgaaattattcaattctagtgctgaacatgattctagtg--ctgaacatgcttctcaaacactg-atggcactgcattaggatctgctaaatatataaaaacctctctatgtag
 |||||  ||  | |||| || || |||| |||||||||||| ||||||||  |||| ||||||||||| |||||||| || || |||||||| |||||||||||     |||| | |  || || | |||||  |   ||      ||  ||||  ||||| |   ||||   | ||  || | |  || || |                                             
AGAAAGGCCCACACAATCAAGAGTTGTTATTTTGTTCAGGGATAGACCATCCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcagtattacgttattcaattaaaattcataggtttctac-ctctacatacttctaataaactgactttactaatctatcgatgtatag---------------------------------------------
















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|71301931|gb|DR787043.1|DR787043
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|91053130|gb|EB163548.1|EB163548
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|18168089|gb|BM337929.1|BM337929
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|12045742|gb|BF727881.1|BF727881
EST:     CAACTACGCAGGATCCCCAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|32789609|gb|CD941845.1|CD941845
EST:     GATCCCCAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTA
genomic: GATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTA
EST: gi|5650101|gb|AI920461.1|AI920461
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|71770870|gb|DR968807.1|DR968807
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|71313708|gb|DR793441.1|DR793441
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|71301929|gb|DR787042.1|DR787042
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|76286156|gb|DV025724.1|DV025724
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|78021692|gb|DV490079.1|DV490079
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|149088757|gb|EE177881.2|EE177881
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|94478107|gb|EB707065.1|EB707065
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGCCAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|6859834|gb|AW355828.1|AW355828
EST:     CAACTACGCAGGATCCCCAGTGGAGGGCAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGGCAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|6828037|gb|AW331680.1|AW331680
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|78083959|gb|DV512352.1|DV512352
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGGTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACTTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|60345336|gb|DN212309.1|DN212309
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|78122117|gb|DV540501.1|DV540501
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|94478108|gb|EB707066.1|EB707066
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|88749980|gb|DY534121.1|DY534121
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|32867214|gb|CF006896.1|CF006896
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|76286157|gb|DV025725.1|DV025725
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|91053129|gb|EB163547.1|EB163547
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|91052960|gb|EB163378.1|EB163378
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|78179907|gb|DV550280.1|DV550280
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|91873772|gb|EB403729.1|EB403729
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|32799538|gb|CD951774.1|CD951774
EST:     GATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTA
genomic: GATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTA
EST: gi|101385884|gb|EB814990.1|EB814990
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|32867213|gb|CF006895.1|CF006895
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|60354545|gb|DN221518.1|DN221518
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|78079632|gb|DV508044.1|DV508044
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|78105386|gb|DV523804.1|DV523804
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|5525617|gb|AI861510.1|AI861510
EST:     CAACTACGCAGGATCCCCAGTGGAGGGCAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGCCAAACCATCGCCAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|91052961|gb|EB163379.1|EB163379
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|148962185|gb|EE013000.2|EE013000
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
EST: gi|149089186|gb|EE178375.2|EE178375
EST:     CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAG                         GCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA
genomic: CAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccaga ... ctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAAGATCCGTAGAATCGAGGGTGGTTACTTTGTTCAGGGAAAGACCATCAACTACGCAGGATCCACAGTGGAGGACAGCTGTCACATCCTCAAACAAGgtactccagatatttcatccttaaaatgaaattattcaattctagtgctgaacatgattctagtgctgaacatgcttctcaaacactgatggcactgcattaggatctgctaaatatataaaaacctctctatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG