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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtttacgaggcataaatttggatagcaacaaaaaggatttggctctcagtctcatgggattctggcttacctcctcgttatcttgctcaatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTGTTTGCTACTGAAGCTTTGCTTGCAGAGCATGGCAAAGGCATTGCAGGCC

Basic information

species Zea mays
transcript GRMZM2G178415_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------tttgtttacgaggcataaatttggatag--caacaaaaaggatttggctct--cagtctcatgg--gattctggcttacctcctcgttat------cttgctcaatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTGTTTGCTACTGAAGCTTTGCTTGCAGAGCATGGCAAAGGCATTGCAGGCC
                                                                                    || |  ||  ||||   || | ||  |     | ||| ||| || |    ||| | |||   |  ||   ||||     | |  ||       ||||||||||||  |||||| ||||||||| | |||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||| ||||
gtaagtatcatgtctagcactttttatcatgttgatgtaatgagaatgatgtttccatgaaaatggattatttcatgggggaatttcataagaaataa---tgaacagtcctttggatagggtttagcaccagtagtattatgactgtctcacacttatgatttggcaatgaaatttttgctcaataca--gGACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTGTTTGCTACTGAAGCCTTGCTTGCAGAGCATGGCAAGGGCATTGCTGGCC

upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 4
tttgtttacgaggcataaatttggatagcaacaaaaaggatttggctctcagtctcatgggattctggcttacctcctcgtt--atcttgctcaatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTGTTTGCTACTGAAGCTTTGCTTGCAGAGCATGGCAAAGGCATTGCAGGCC
                    |  |  |  || ||  |  || | | | |    || |||      |     ||||    |||  ||  || | |  |  ||||| || || |||||  | || |||||||| ||||||||||| |||||  |||||| ||| ||||||||||||   ||||| || ||   |||  |||| |
-------------------gtaagtaaagaataatcacaatcttgttttg---ctaatgactggtttaaccacctgaatgtttaatgatgtttatgaaccagGATCTTGGTGGATCGCTAGGGAGAGACGCGGCTACTGGAAGAGGAGTGATGTTTGGTACCGAAGCTTTGCTTAACGAGCACGGAAAGACCATATCAGGGC
















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|211300259|gb|FL012334.1|FL012334
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|19436213|gb|BM952623.1|BM952623
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|13125987|gb|BG316662.1|BG316662
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|19351121|gb|BM895653.1|BM895653
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|148934217|gb|EC878238.2|EC878238
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
EST: gi|60357158|gb|DN224131.1|DN224131
EST:     ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG                         GACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaact ... caatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcagtctcatgggattctggcttacctcctcgttatcttgctcaatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTGTTTGCTACTGAAGCTTTGCTTGCAGAGCATGGCAAAGGCATTGCAGGCC
                     ggcttac  putative branch site (score: 3)
                                      tcttgctc  putative PPT
                                   ttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtttacgaggcataaatttggatagcaacaaaaaggatttggctctcagtctcatgggattctggcttacctcctcgttatcttgctcaatacacagGACCTCGGAGGATCATTGGGAAGAGACGCCGCTACTGGAAGGGGAGTTCTGTTTGCTACTGAAGCTTTGCTTGCAGAGCATGGCAAAGGCATTGCAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG