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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttattttgttaattgctgaatcttaattttgctgtgtgtcaaatgaaacttctgttattattgaaagttgcttatgttatgtatgattatgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATTTTGCCGCTATCTCTGCCTTGAAAGTT

Basic information

species Zea mays
transcript GRMZM5G840928_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840928_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g17610.1 (Oryza sativa), 3'ss of exon 1
ttttattttgttaattgctgaatcttaattttgctgtgtgtcaaatgaaacttctgtt-attattgaaagttgcttatgttatgtatgat---tatgtc-ctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATTTTGCCGCTATCTCTGCCTTGAAAGTT
 | ||||||     ||| |     || || || |        |||| |   | ||||| |||  | ||  || ||||  |     || ||   ||  |  | ||||||| || || ||||| || |||||||||||||||||||| ||||| |||||||| || || |||||||||||||||
-tgtattttccagtttgttattgtttcatgttcccaaa----aaattagtttcctgttgattccttaagtttacttacatatcaaattatcgatacatttcccagGGAAAATTGCTGTAATTGGTGGATGTCGTGAGTACACTGGTGCTCCCTATTTTGCAGCGATTTCTGCCTTGAAAGTT

upper sequence: GRMZM5G840928_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G19150.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------ttttattttgtta------attgctgaatcttaattttgctgtgtgtcaaa---tgaaacttctgttatta-ttgaaagtt---gcttatgttatgta--tgattatgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATTTTGCCGCTATCTCTGCCTTGAAAGTT
                ||  ||| ||| |      |||  | ||  |  |   |   |  | | |||   |||   || |    ||| ||  | |||   ||| ||||  || |  ||||  |||  |||||||||||||| || || |||||||||||||| ||||| |||||||| || || || || || || || |||||| | 
gttagtgcttgctctattcaattgtgtcatcagaaatttatcaaattcgaaactttaggattttaaagtttgagttttttcaggttactttgatgttttagctcatgtgttggaattgatcttgtg-tcagGGAAGATAGCTGTGATTGGAGGATGTCGTGAATACACAGGAGCTCCATACTTCGCTGCCATTTCAGCTTTGAAAATC
















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|76020592|gb|DT947762.1|DT947762
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|76011915|gb|DT939085.1|DT939085
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|71766337|gb|DR964274.1|DR964274
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|101395549|gb|EB819702.1|EB819702
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|50330426|gb|CO525552.1|CO525552
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|89249729|gb|DY621515.1|DY621515
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|76016158|gb|DT943328.1|DT943328
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|211190739|gb|FL216448.1|FL216448
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|89759085|gb|DY688018.1|DY688018
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|211152681|gb|FL231436.1|FL231436
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|71448822|gb|DR829872.1|DR829872
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|89252939|gb|DY624725.1|DY624725
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|71767740|gb|DR965677.1|DR965677
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|101385680|gb|EB814888.1|EB814888
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|89247422|gb|DY619208.1|DY619208
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|211190744|gb|FL216453.1|FL216453
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|76018446|gb|DT945616.1|DT945616
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|76282804|gb|DV022372.1|DV022372
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|211190740|gb|FL216449.1|FL216449
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|211190742|gb|FL216451.1|FL216451
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|76912720|gb|DV164861.1|DV164861
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
EST: gi|211190743|gb|FL216452.1|FL216452
EST:     GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAG                         GGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT
genomic: GCGCCGGATCACGCCGGCACTCGACCGCGCCAGACACAAGGGCCAGGCAGgtcagtaccg ... atgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaacttctgttattattgaaagttgcttatgttatgtatgattatgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATTTTGCCGCTATCTCTGCCTTGAAAGTT
                                              tgtcctc  CT-rich tract
           ttattattgaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttattttgttaattgctgaatcttaattttgctgtgtgtcaaatgaaacttctgttattattgaaagttgcttatgttatgtatgattatgtcctcagGGAAGATAGCAGTAATCGGAGGATGTCGTGAGTACACTGGAGCTCCTTATTTTGCCGCTATCTCTGCCTTGAAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - -ttttgtt
- - - - - - - -tgctgaa
- - - - - - - - - - - - - - -tttgctg
- - - - - - - - - - - - - - - - - - - - - aaatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtatg