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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctctttctcagtctctgacatatacaaacggtgagcacgcacaagcactgactgaaagttaaacacatgattttgcag

Basic information

species Zea mays
transcript GRMZM2G330650_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330650_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g25390.3 (Oryza sativa), 5'ss of exon 6
-------ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccc---tctttctcagtctctgacatatacaaacggtga-gcacgcacaagcactgactgaaagttaaacacatgattttgcag
       ||||| ||||||||||||||||| |||||||| |||||||| ||||| ||  | ||||| |||||||| || ||||| |||||||| || |||| || |||    || ||||   |     | |   |    | |   ||| |  || ||| |  |||||| || ||  |      ||||||
TTTACAGACAGAACAAATGAAGAGAATTGGCAATGAGCTGGATACTGTTCACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccatccctctctcttccctctgcgtgcgcttgtgcttttgcatgtcca-gcagtacctgaaatttgaaatc-----cttgcag

upper sequence: GRMZM2G330650_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g25390.1 (Oryza sativa), 5'ss of exon 8
ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccc---tctttctcagtctctgacatatacaaacggtga-gcacgcacaagcactgactgaaagttaaacacatgattttgcag
||||| ||||||||||||||||| |||||||| |||||||| ||||| ||  | ||||| |||||||| || ||||| |||||||| || |||| || |||    || ||||   |     | |   |    | |   ||| |  || ||| |  |||||| || ||  |      ||||||
ACAGAACAAATGAAGAGAATTGGCAATGAGCTGGATACTGTTCACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccatccctctctcttccctctgcgtgcgcttgtgcttttgcatgtcca-gcagtacctgaaatttgaaatc-----cttgcag
















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|71774532|gb|DR972410.1|DR972410
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGG
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGG
EST: gi|60396385|gb|DN229254.1|DN229254
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|32866170|gb|CF005852.1|CF005852
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTTCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|71774531|gb|DR972409.1|DR972409
EST:     ACTTCTCCCTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|148991480|gb|EE032993.2|EE032993
EST:     ACTTCTCCCTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|50338100|gb|CO533226.1|CO533226
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|76286033|gb|DV025601.1|DV025601
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|21810005|gb|BQ668323.1|BQ668323
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTTCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|71442678|gb|DR823728.1|DR823728
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|60396054|gb|DN228924.1|DN228924
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|211141939|gb|FL417378.1|FL417378
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCTTGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|33467215|gb|CF244264.1|CF244264
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|87157738|gb|DY402527.1|DY402527
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTTCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|89754547|gb|DY685289.1|DY685289
EST:     ACTTCTCCCTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|7135269|gb|AW498001.1|AW498001
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTTCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|7135591|gb|AW498164.1|AW498164
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTTCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|18166041|gb|BM335880.1|BM335880
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|78074383|gb|DV502817.1|DV502817
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|86468443|gb|DY234813.1|DY234813
EST:     AGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTTTTCCTGATCGTTTTGGGT
genomic: AGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|78122352|gb|DV540736.1|DV540736
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|71306394|gb|DR789339.1|DR789339
EST:     ACTTTTCCCTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|60337886|gb|DN204859.1|DN204859
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|110510919|gb|EE019261.1|EE019261
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|148961350|gb|EE012080.2|EE012080
EST:     CTTCTCACCTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCAT
genomic: CTTCTCAC-TGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCAT
EST: gi|76019098|gb|DT946268.1|DT946268
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctctttctcagtctctgacatatacaaacggtgagcacgcacaagcactgactgaaagttaaacacatgattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT