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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactctgttctgttgtgccatgctttaatgcttaggaatcatgtagatgtcataacctggcttgtaatgtaatatggttatcatcgcacttgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAGTTTGACTATGACCTAAAGCAG

Basic information

species Zea mays
transcript GRMZM2G081188_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 3'ss of exon 3
tactctgttctgttgtgccatgctttaatgcttaggaatcatgtagatgtcataacctggcttgtaatgtaatatg-gttatcatcgcacttgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAGTTTGACTATGACCTAAAGCAG
|   |||||   || |    |  | | || ||||| ||  | ||||   |  ||| ||  |||||||| ||||||| ||| |  |    ||  | |  ||||||||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
tttcctgttg-attatattttcttcttatccttagcaacaaagtaggcattttaatctaccttgtaatataatatgagttcttgttatgctattgcttcagGATGGTGCAGGTCGTGTCGGAAAAATGCTTTTTGCACGTCAAGGAAAGAAGTTTGACTATGACCTAAAGCAG

upper sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 3
tactctgttctgttgtgccatgctttaatgcttaggaatcatgtagatgtcat----aacctggcttg-taatgtaatat-ggttatcatcgcacttgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAGTTTGACTATGACCTAAAGCAG
   | |  | | | ||   || |||| |||| |        | ||    || |    ||| ||||||  | |   | | | |  |||||  | | || |     ||||||||||||||||||| |||||||||||||||||  | || |||||||| ||||| |||||  | || |||
-gttttcctttctcgtat-atcctttcatgcatcatgcatgtataacaatcctttaaaacatggcttactcactcattgttgaatatcaatgtaattct--tgtagGATGGTGCTGGGCGTGTTGGGAAAATGCTTTTTGCGAGGCAGGGAAAGAAATTTGATTATGATTTGAAACAG

upper sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
tactctgttctgttgtgccatgctttaatgcttaggaatcatgtagatgtcataacctggcttgtaatgtaatatggt-----tatcatcgcacttgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAGTTTGACTATGACCTAAAGCAG
   | || | | | |  || |  |||     || | | | |  |  |||  ||||      ||| ||||  || || |     ||   |  || |       |||||||||||||| ||||| |||||||||||||||||||| ||||| ||||||||||| ||||| ||||| |||
---tttgctttatgg--ccttcttttttcagtttgaatttagcttcatggaataattgcatttgaaatgatatttgttgaatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG

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|148945695|gb|EC890968.2|EC890968
EST:     CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAG                         GATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
genomic: CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAGgtaaaaacat ... tgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
EST: gi|148953714|gb|EC899078.2|EC899078
EST:     CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAG                         GATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
genomic: CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAGgtaaaaacat ... tgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
EST: gi|32837137|gb|CD976815.1|CD976815
EST:     CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAG                         GATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
genomic: CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAGgtaaaaacat ... tgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
EST: gi|149076159|gb|EE164750.2|EE164750
EST:     CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAG                         GATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAGGGAAAGAAG
genomic: CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAGgtaaaaacat ... tgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
EST: gi|31353527|gb|CD437884.1|CD437884
EST:     CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAG                         GATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
genomic: CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAGgtaaaaacat ... tgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
EST: gi|148958478|gb|EC904716.2|EC904716
EST:     CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAG                         GATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
genomic: CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAGgtaaaaacat ... tgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
EST: gi|148966241|gb|EE017202.2|EE017202
EST:     CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAG                         GATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
genomic: CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAGgtaaaaacat ... tgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
EST: gi|211296912|gb|FL058764.1|FL058764
EST:     CTCAAAGCAAGGTAACACCANGTGTCATTGCTATCAACTGGATCCTCAGG                         GATGGTGCTTGGCGTGTCGGGAAAATGCTTTTTGCCCCGTCA-GGAAAGA-
genomic: CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAGgtaaaaacat ... tgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCAC-GTCAAGGAAAGAA
EST: gi|149012213|gb|EE042512.2|EE042512
EST:     CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAG                         GATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG
genomic: CTCAAAGCAAGGTAACACCAGGTGCCATTGCTATCAACTGGATCCTCAAGgtaaaaacat ... tgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtcataacctggcttgtaatgtaatatggttatcatcgcacttgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAGTTTGACTATGACCTAAAGCAG
    tcataac  putative branch site (score: 2)
                ttgtaatgtaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactctgttctgttgtgccatgctttaatgcttaggaatcatgtagatgtcataacctggcttgtaatgtaatatggttatcatcgcacttgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAGTTTGACTATGACCTAAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT