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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccacctgctagctcatgcttattcctctcttcaatttcttatggatttgtgtttgtctgtacgtgattcctgggtcgcaaaaccaaatcaaattatctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGACCACGAGGGCGCAGCTGCTCCTGCCGCCGCCGCCGCCTCCTCCTCCTAC

Basic information

species Zea mays
transcript GRMZM2G116185_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116185_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g50900.1 (Oryza sativa), 3'ss of exon 2
gtaccacctgctagctcatgcttattcctctcttcaatttcttatggatttgtgtttgtctgtacgtgattcctgggtcgcaaaaccaaatcaaattatctg-----tgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGACCACGAGGGCGCAGCTGCTCCTGCCGCCGCCGCCGCCTCCTCCTCCTAC
             | |  |||    || |||      || |||||| |||||| ||||| |||   | | | |  | | |  |  |    |     | |         ||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||| | || | ||| ||||||    | | | ||   |  |    
-------------gttggtgcaggatcttct------ttccttatgcatttgtatttgtttgttgattaattcgtgtttgtgattcatcttgggggtttacaaaactcgcctagGATCCTGGCATGGGAGGATGGATTCTGCAACTTTGCAGCCTCTGCCTGTGACCAAGAGGACACACCAGCTGCTGCCGGGTACACTGACTATGCAGCAGCT

upper sequence: GRMZM2G116185_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g07950.t01 (Vitis vinifera), 3'ss of exon 2
gtaccacctgctagctcatgcttattcctctcttcaatttcttatggatttgtgtttgtctgtacgtgattcctgggtcgcaaaaccaaatcaaattatctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGACCACGAGGGCGCAGCTGCTCCTGCCGCCGCCGCCGCCTCCTCCTCCTAC
                  |  | | |      ||  |||| || | | ||| ||    ||   | |   |   |   | | |    |        |||      |||||||| |||| |||||||||||| ||||||||||||    | ||  ||  |||     |    | ||| |   |  | |    |     |||          
-----------------gtattcactaggaagtttcattt-ttctagttttctgcac-tccccaagctttatttcacttgaatggtctttcatggttagtatgtcccagGATACTGGTATGGGAGGATGGCTTCTGCAACTTCATTCCTTCAACCACTGAGATTAATCCTGGAGCAGGATCCTCAGTTCACAGAAACTCTGAAGTTAGA
















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|78086977|gb|DV515370.1|DV515370
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|71441212|gb|DR822262.1|DR822262
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|78092358|gb|DV520732.1|DV520732
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|71299046|gb|DR785511.1|DR785511
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|91055983|gb|EB166401.1|EB166401
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|101385166|gb|EB814629.1|EB814629
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|76291869|gb|DV031437.1|DV031437
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|71316518|gb|DR794933.1|DR794933
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|20803186|gb|BQ294236.1|BQ294236
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGTCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|148953903|gb|EC899284.2|EC899284
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|76934748|gb|DV174011.1|DV174011
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|50336434|gb|CO531560.1|CO531560
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGNCA-CTTCGCAGCCTCTGCCTGTG
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTG-CAACTTCGCAGCCTCTGCCTGTG
EST: gi|91049965|gb|EB160383.1|EB160383
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|86472078|gb|DY238448.1|DY238448
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGTGTGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGAGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|71442162|gb|DR823212.1|DR823212
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|26456486|gb|CA828069.1|CA828069
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|78084497|gb|DV512890.1|DV512890
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|93012864|gb|EB638384.1|EB638384
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|149109966|gb|EE293776.2|EE293776
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|101393159|gb|EB818510.1|EB818510
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|50330625|gb|CO525751.1|CO525751
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|76014748|gb|DT941918.1|DT941918
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
EST: gi|101395608|gb|EB819733.1|EB819733
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCCTGCA-CTTCCCAGCCTCTGCCTGTG
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTC-TGCAACTTCGCAGCCTCTGCCTGTG
EST: gi|78112591|gb|DV530985.1|DV530985
EST:     GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTG                         GATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA
genomic: GATCTCCAGGGCGGCATATACGACCGGACAAGAGGGAACAGGAGGAACTGgtaccacctg ... ctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtctgtacgtgattcctgggtcgcaaaaccaaatcaaattatctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGACCACGAGGGCGCAGCTGCTCCTGCCGCCGCCGCCGCCTCCTCCTCCTAC
                                 aaatcaaattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccacctgctagctcatgcttattcctctcttcaatttcttatggatttgtgtttgtctgtacgtgattcctgggtcgcaaaaccaaatcaaattatctgtgcccagGATCCTGGCATGGGAGGATGGATTCTGCAACTTCGCAGCCTCTGCCTGTGACCACGAGGGCGCAGCTGCTCCTGCCGCCGCCGCCGCCTCCTCCTCCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC