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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacatccgttctctctggtcactgtcgtttttcgcgtcgtctctccggatctgaccttctgttttcggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAGCGCAGCTCAAGGAGCTTAAATCGGAGCTCTCCCTCCTACGCGTCGCCAA

Basic information

species Zea mays
transcript GRMZM2G010599_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010599_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g30730.1 (Oryza sativa), 3'ss of exon 1
gtaagcacatccgttctctc------------tggtcactgtcgtttttcgcgtc---gtctctccggatctgaccttctgtttt-cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAGCGCAGCTCAAGGAGCTTAAATCGGAGCTCTCCCTCCTACGCGTCGCCAA
||||||    || | |||||            |  || |  |   |||| ||        |  ||||||||||||| | | ||   |   |  ||||||||||||||||||||||||| || || |||| |||| |||| ||||| || ||||||||||| || ||  |||||||||||||||| |||||||||||
gtaagcctccccctcctctccctctctccggttcatctcgattagttttagctctcaatcccttccggatctgaccgtttcttggacaaatgtcagCCCGGATCAAGGTGCACGAGCTCCGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA

upper sequence: GRMZM2G010599_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g30050.1 (Oryza sativa), 3'ss of exon 1
gtaagcacatccgttctctctggtcactgtcgtttttcgcgtcgtctctccggatctgaccttctgttttcggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAGCGCAGCTCAAGGAGCTTAAATCGGAGCTCTCCCTCCTACGCGTCGCCAA
||||||     | |||      ||   | ||   |  ||| ||| ||   ||||||| ||| |  || |  |||  |||||||||||||||||  ||||||| || || |||| |||| |||| ||||| || ||||||||||| || ||  |||||||||||||||| |||||||||||
gtaagctacaacattcc-----gttcttctctcctcccgc-tcgcctg--cggatctaaccgtgcgtgtgtggt--gcagCCCGGATCAAGGTCGACGAGCTACGGGGGAAGAACAAGGCGGAGCTGCAGGCCCAGCTCAAGGACCTCAAGGCGGAGCTCTCCCTCCTCCGCGTCGCCAA
















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|211328828|gb|FK988192.1|FK988192
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211335323|gb|FK988235.1|FK988235
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|67020323|gb|CO449072.1|CO449072
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211328832|gb|FK988196.1|FK988196
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|89755381|gb|DY685822.1|DY685822
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|60400231|gb|DN233038.1|DN233038
EST:     CTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: CTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|32930463|gb|CF035275.1|CF035275
EST:     TTTTCATCTCATTCGGCGCCGCGGCGCCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|67023749|gb|CO452498.1|CO452498
EST:     GCGCCGTGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: GCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|67023906|gb|CO452655.1|CO452655
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|18176750|gb|BM351683.1|BM351683
EST:     CGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: CGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211250381|gb|FL431483.1|FL431483
EST:     CCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: CCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|30704600|gb|CD058563.1|CD058563
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|30307036|gb|CD001709.1|CD001709
EST:     TTTTCATCTCATTCGG-GCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211333157|gb|FK988224.1|FK988224
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211254801|gb|FL420516.1|FL420516
EST:     ACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: ACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211333150|gb|FK988217.1|FK988217
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|4730667|gb|AI649833.1|AI649833
EST:     CATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: CATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211333162|gb|FK988229.1|FK988229
EST:     TTTTCATCTCATTCGGCGCCGCGG--CTCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|67022317|gb|CO451066.1|CO451066
EST:     TTTTTATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211330991|gb|FK988208.1|FK988208
EST:     TTTTCATCTCATTCGGCGCCGCGG--CTCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|30704590|gb|CD058562.1|CD058562
EST:     TCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211335320|gb|FK988232.1|FK988232
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211330996|gb|FK988213.1|FK988213
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211441107|gb|FL033103.1|FL033103
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
EST: gi|211330990|gb|FK988207.1|FK988207
EST:     TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGG                         CCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG
genomic: TTTTCATCTCATTCGGCGCCGCGGCACCCCCTGCTCGTCACTCGCGATGGgtaagcacat ... cggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtcgtttttcgcgtcgtctctccggatctgaccttctgttttcggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAGCGCAGCTCAAGGAGCTTAAATCGGAGCTCTCCCTCCTACGCGTCGCCAA
                            atctgac  putative branch site (score: 3)
                                  ccttctgttttc  CT-rich tract
       ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacatccgttctctctggtcactgtcgtttttcgcgtcgtctctccggatctgaccttctgttttcggttcgcagCCCGGATCAAGGTGCACGAGCTGCGCGGAAAGAGCAAGACGGATCTGCAAGCGCAGCTCAAGGAGCTTAAATCGGAGCTCTCCCTCCTACGCGTCGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT