Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taataatactatgttacttgctcagtacttttatctgtagaatctacaaaacactgcatttgtctaatgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG

Basic information

species Zea mays
transcript GRMZM2G015344_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 3
taataatactatgttacttgctcagtacttttatctgtagaatcta--caaaacactgcatttgtcta-atgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG
    |   |    || |   |  | ||| |||     |  | || |  |||  | |     || |||  |||| ||   | ||       |  ||| | |||||||||| |||| ||||||||||| || ||||||||||| |||||| | |||||| ||||||||||||||||| ||  |||||||||||| |||| |||||
---gaccgcagacttccgatcatactacatttcctattcaattccagtcaacgccccatgcttatctggatgagcttgttaatgatgtgctcttgtactttagGGAGGAGAGCCACGTGTTGCTGACTTTGTTCATGGGTCTGATGGCCTGGGGAATTTGTTTCTTCCTGCACCCACTAGTAAGAAGGTTGATGAAAATGCTG

upper sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G35170.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------taata-atactatgttacttgctcagtactttta---tctgtagaatctacaaaacactgcattt---gtctaatgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG
                                                                  ||     || ||||    |||   | |  ||    || |    ||||        ||   |||   ||    |||  | ||| || |||   || | | ||  |||| |||||||| |||||||||||||| ||||||||   ||||||  | |||||    || || ||  ||||    | | ||||  ||||| |||||||| 
gtaactattttaatgtgtagatttagcttctctaatgttgattcggtcaatttaggttttaattggatgtgggctttgttttcggctacatccaattgaactcggcctgatctgacttctcctcttttttttgttctctgatattaattat-gatttattttctgcaaaagGGTGGAAAGCCTCGTGTTGCTGATTTTGTTCATGGTAAAGATGGACTAGGGAACACATTCCTACCCCCACCTAAAGGTGAGAAAATTGAGAAAAGTGCTA
















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|89759746|gb|DY688465.1|DY688465
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|89251363|gb|DY623149.1|DY623149
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|211057429|gb|FL062177.1|FL062177
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCC-GTGTTGCTGATTTCGTTCA
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCA
EST: gi|71318567|gb|DR796043.1|DR796043
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|71449461|gb|DR830511.1|DR830511
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|51871130|gb|CV126014.1|CV126014
EST:     CAGGACACCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTTGTTCATGGGTCAGACGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|76935894|gb|DV174515.1|DV174515
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|32803180|gb|CD955416.1|CD955416
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|71438819|gb|DR819869.1|DR819869
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|78105410|gb|DV523828.1|DV523828
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|94473161|gb|EB702119.1|EB702119
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|149077634|gb|EE166336.2|EE166336
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|76290576|gb|DV030144.1|DV030144
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|211054466|gb|FL062172.1|FL062172
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTCGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|211057438|gb|FL062186.1|FL062186
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGA
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGA
EST: gi|71439185|gb|DR820235.1|DR820235
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
EST: gi|211057431|gb|FL062179.1|FL062179
EST:     CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG                         GGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaaacactgcatttgtctaatgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG
                gtctaat  putative branch site (score: 3)
                   taatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taataatactatgttacttgctcagtacttttatctgtagaatctacaaaacactgcatttgtctaatgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTGTTGCTGATTTCGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG