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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgccattaaattctagtcttggtttctgttcatggttattttggcataagatgtgtgctgaatgctgattgtctaatttttgcattggattggaacatatctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGAGCAAGAG

Basic information

species Zea mays
transcript GRMZM2G094595_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094595_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 5
--------------------gttctgccattaaattctagt---cttggtttctg-----ttcatggttattttggcataagatgtgtgctgaatgctgattgtctaatttttgca-ttggattggaacatatctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGAGCAAGAG
                    | ||   ||||   |   ||    ||| |   |       |||||||| || ||     ||||||||||||   |      | || || | || || ||| |||| || |  ||  || ||||||||||| || ||| || | |||||||||||| |||| ||||||||||||||||||
gttctgttttttaacttggtgatccagcattggttggaagcaagcttagcgccattaaatttcatggt-atctttatgcaagatgtgtgct---tatatgctttccaactcttacagttgaattgcaaaacttccatgcagTGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGAGCAAGAG
















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|9952612|gb|BE639300.1|BE639300
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|71441037|gb|DR822087.1|DR822087
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|211518545|gb|FL166760.1|FL166760
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|211141663|gb|FL166772.1|FL166772
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|211518549|gb|FL166764.1|FL166764
EST:     GCGCACACTGACAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|211518548|gb|FL166763.1|FL166763
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|211518551|gb|FL166766.1|FL166766
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCAC
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCAC
EST: gi|211518552|gb|FL166767.1|FL166767
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|78089821|gb|DV518195.1|DV518195
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|78086538|gb|DV514931.1|DV514931
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|9952213|gb|BE638796.1|BE638796
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|32788291|gb|CD940527.1|CD940527
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTA
EST: gi|211518553|gb|FL166768.1|FL166768
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATGGTGCGGGCGCTGA-GGAAAAGCTTG
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCC-CTGAAGGAAAAGCTTG
EST: gi|211518555|gb|FL166770.1|FL166770
EST:     GCGCACACTGAGAAGTACCCCGATGAAYCTCCACTACTAAATGTGAAAAG                         TGYACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAG
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAG
EST: gi|211141662|gb|FL166771.1|FL166771
EST:     CGCACACTGAGAAGTACCCCGATGAACCTCCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTT
genomic: CGCACACTGAGAAGTACCCCGATGAACCTCC-ACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTT
EST: gi|89760930|gb|DY689145.1|DY689145
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|211518550|gb|FL166765.1|FL166765
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|211518546|gb|FL166761.1|FL166761
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|14202224|gb|BG835901.1|BG835901
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
EST: gi|211141664|gb|FL166773.1|FL166773
EST:     GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAG                         TGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA
genomic: GCGCACACTGAGAAGTACCCCGATGAACCTCCACTACTAAATGTGAAAAGgttctgccat ... atctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgctgaatgctgattgtctaatttttgcattggattggaacatatctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGAGCAAGAG
                 gtctaat  putative branch site (score: 3)
              attgtctaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctgccattaaattctagtcttggtttctgttcatggttattttggcataagatgtgtgctgaatgctgattgtctaatttttgcattggattggaacatatctgtgtagTGTACGAGGGATTAAACCACATGATCTTGCATCCCTGAAGGAAAAGCTTGAGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA