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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgctcttatctcccttcatgctgctaagtgctgagctttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC

Basic information

species Zea mays
transcript GRMZM2G149272_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g42520.3 (Oryza sativa), 3'ss of exon 3
-------------gtgcgctcttatct-----cccttcatgctgctaagtgctgagctttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC
              |     || ||||      |  |  ||||| |    ||   |  | |||| |||||   || | ||| ||  |        ||||   | ||| | ||| || || |||||||| ||||||||||||||||||||| |||| || ||||| || ||||| |||||||| || || |||| |||||||||||||||||| 
gtctgtatagtctatatatactgatctagcagtctcttttgctgttgc-cgccatgtctcgcaagttgctcggaacactgacattgg--------aacgatct-gatgtgtagTGTGGTTGAGAGTGTTGGTGAAGGTGTGACCGAGTTCGAAGTGGGAGACCATGTGCTCACCGTCTTCATCGGAGAGTGCATGAGCTGCAAGCACTGCGTT
















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|78087348|gb|DV515741.1|DV515741
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211026991|gb|FL377493.1|FL377493
EST:     C-G-C--AACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|89755821|gb|DY686098.1|DY686098
EST:     C-G-C--AACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|71769715|gb|DR967652.1|DR967652
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211199112|gb|FL383376.1|FL383376
EST:     C-G-C--AACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|89252932|gb|DY624718.1|DY624718
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|71448196|gb|DR829246.1|DR829246
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|149083974|gb|EE173360.2|EE173360
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211284822|gb|FL429278.1|FL429278
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211284823|gb|FL429279.1|FL429279
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|29946549|gb|CB816205.1|CB816205
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211323238|gb|FL374213.1|FL374213
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|71331903|gb|DR802837.1|DR802837
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211539558|gb|FL409998.1|FL409998
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|50322631|gb|CO517757.1|CO517757
EST:     GCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: GCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211228051|gb|FL407860.1|FL407860
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|71325644|gb|DR799509.1|DR799509
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|148963165|gb|EE014137.2|EE014137
EST:     CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|93016182|gb|EB641702.1|EB641702
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|211063859|gb|FL423538.1|FL423538
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|76016068|gb|DT943238.1|DT943238
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|101382109|gb|EB813110.1|EB813110
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     -AGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGG                         AGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA
genomic: CAGGCGCAACTTGATCTGTTCCCCAGAGTCTTCGGCCACGAGGCATCCGGgtgcgctctt ... cgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC
                                       cgccttc  CT-rich tract
           ttctaataatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgctcttatctcccttcatgctgctaagtgctgagctttgcaaattgcttctaataatgatatctgttgacctgaacgccttcgatctatagAGTAGTAGAGAGTGTCGGTGAAGGTGTGACCGAGTTCCAAGTCGGTGACCACGTTCTCACTGTCTTCATTGGGGAATGCAAGAGCTGCAAGCACTGCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC