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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtaggtttatttaattctctttccttgaattcttctatctcagaaagaccagaactgattttttttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG

Basic information

species Zea mays
transcript GRMZM2G057412_T04
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057412_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g33590.1 (Oryza sativa), 3'ss of exon 8
gtgtaggtttatttaattctcttt---ccttgaattcttctatctcagaaagaccaga--actgattttttttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG
|| ||  ||||||  |||||  ||    | |||||  ||  ||  |        | ||  |   | ||   |||| | |||| ||||||||||| ||||||||||||||| ||| |||||||| |||| ||||||||||||||||||||||||||||||||||||
gtctaactttattgtattcttgttgtatcatgaatgttttaatagcttttttttctgatcatctaattaccttttttgcagACTGGTGAGTGCCTTGAAGAATCACTTAGAATTGCAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG
















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|74240130|gb|DT648044.1|DT648044
EST:     CGAATCTCAGATTTTATTAAG                         AATGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: CGAATCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
EST: gi|93281097|gb|EB673361.1|EB673361
EST:     ATTTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAG                         AGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
EST: gi|149102607|gb|EE287965.2|EE287965
EST:     ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAG                         AGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
EST: gi|33467969|gb|CF245018.1|CF245018
EST:     TCTCAGATTTTATTAAG                         AGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: TCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
EST: gi|76909352|gb|DV163342.1|DV163342
EST:     ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAG                         AGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
EST: gi|211386247|gb|FL227579.1|FL227579
EST:     ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAG                         AGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
EST: gi|74242217|gb|DT650131.1|DT650131
EST:     ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAG                         AGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
EST: gi|60347261|gb|DN214234.1|DN214234
EST:     TCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAG                         AGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: TCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
EST: gi|89759386|gb|DY688239.1|DY688239
EST:     ATCTTAATGATCAGAGAGACCTGTTCCAACGAATTTCAGATTTTATTAAG                         AGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
EST: gi|60354297|gb|DN221270.1|DN221270
EST:     ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAG                         AGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT
genomic: ATCTTAATGATCAGAGAGACCTGTTCCAACGAATCTCAGATTTTATTAAGgtgtaggttt ... ttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccttgaattcttctatctcagaaagaccagaactgattttttttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG
                                 aactgat  putative branch site (score: 3)
                                   ctgattttttttttct  CT-rich tract
                                 aactgatttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtaggtttatttaattctctttccttgaattcttctatctcagaaagaccagaactgattttttttttctccagAGTGGTGAGTGCCCTGAAGAATCACTTAGGATTTCAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA