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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAAGAGGTTGTAACTCCATGGTTTAAGTTCCTCTGGGAGACATACAGGACTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctattctcttatgagcattttgttgcttgcttctgttgaatttactttgtatgtggcacataaattttccatggtattggtacaacacattacca...

Basic information

species Zea mays
transcript GRMZM2G093050_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093050_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g03070.1 (Oryza sativa), 5'ss of exon 3
TAAAGAGGTTGTAACTCCATGGTTTAAGTTCCTCTGGGAGACATACAGGACTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctattct-cttatgagcattttgttgcttgcttctgttgaatttactttgtatgtggcacataaattttccatggtattggtacaacacattacca--
 | ||||  ||| || |||||||| ||||| |||||||| |||||||| || ||||| |||||| | || |||||||||||||||||||| |||||||||||||||||||||   | ||  |   || || | ||  |   |    || ||     |  |||||  | |  |  |  |   |||  |     |||  | ||  
CAGAGAGCATGTCACACCATGGTTCAAGTTTCTCTGGGAAACATACAGAACAGTTCTTGAGATATTGAGAAACAATTCAAAGCTTGAAGCATTATATGCTgtaagctattctatctgtgttccccttatt-cctgtatacatactcttcacacatgacatggcatttcatctggctgttccatt--ttgtgtacacaatcaat

upper sequence: GRMZM2G093050_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G32950.3 (Glycine max), 5'ss of exon 2
TAAAGAGGTTGTAACTCCATGGTTTAAGTTCCTCTGGGAGACATACAGGACTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctattctcttatgagcattttgttgcttgcttctgttgaatttactttgtatgtggcacataaattttcc--atggtattggtacaacacattacca
|   |||  ||| || |||||||||||||| || ||||| || || ||||| || || || ||| | |||||||| |||||||| ||||| ||||||||||||| || |  |||||||  | || |    |||  |  || |  |  |  ||  |||||      | ||| | |   ||  |  | || |   |  |||   
TCGGGAGACTGTGACCCCATGGTTTAAGTTTCTTTGGGAAACTTATAGGACAGTGCTGGAAATATTGAGGAACAACTCAAAGCTAGAAGCCTTATATGCTgtaatctttcttcttatgttc-ttgtacaacttcttgatgctatacatgattcatatgtatttgcttaatgtacagaattatgcttgttct-tatcttattc

upper sequence: GRMZM2G093050_T04 (Zea mays), 5'ss of exon 3
lower sequence: AT4G11420.1 (Arabidopsis thaliana), 5'ss of exon 3
TAAAGAGGTTGTAACTCCATGGTTTAAGTTCCTCTGGGAGACATACAGGACTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctattctcttatgagcattttgttgcttgcttctgttgaatttactttgtatgtggcacataaattttccatggtattggtacaacacattacca
    ||| | || || |||||||||||||| || ||||||||||||||||| || || |||||| |  | ||||| |||||| | |||||  | ||||| ||  | | ||||  || |   |  || ||| | | | |   ||| ||||  |||  || |    |  | || | | |  || |  |  |           
CCGTGAGTTGGTCACCCCATGGTTTAAGTTTCTGTGGGAGACATACAGGACAGTCCTTGAGATATTGCGAAACAACTCAAAGTTGGAAGCACTTTATGCGgtttgtt-ttcttctaggttaagcttattggt-gatacctctgattttaagttgattgagattgaagacttgtactttataatcttgtag----------

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|211266092|gb|FL146493.1|FL146493
EST:     TTCTAGAGATACTAAAGGA-CAATTTCAA-GCTTGAAGCCGT-ATATGCT                         ATGACGGCTCATAGGGCTTTTCAATTCTGTAAA-AGTA
genomic: TTCTAGAGATACTAA-GGAACAATT-CAAAGCTTGAAGC-GTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTA
EST: gi|32929632|gb|CF034444.1|CF034444
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
EST: gi|67019799|gb|CO448548.1|CO448548
EST:     GTTCTAGAGATACTANAGGGACA-TTCANAGCTTGAAAGCGT-ATATGCT                         ATGACTGCTCATAGGGCTT
genomic: GTTCTAGAGATACTA-AGGAACAATTCAAAGCTTGAA-GCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTT
EST: gi|22543324|gb|BU093762.1|BU093762
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
EST: gi|26457299|gb|CA828882.1|CA828882
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
EST: gi|31361475|gb|CD445832.1|CD445832
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
EST: gi|32934017|gb|CF038829.1|CF038829
EST:     AAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: AAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
EST: gi|211268529|gb|FL146508.1|FL146508
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATANGGCTTTTTCA-TTCTGTAAACAGTATAAGAGA-CAAC
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTT-CAATTCTGTAAACAGTATAAGAGAACAAC
EST: gi|211266101|gb|FL146502.1|FL146502
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
EST: gi|148930736|gb|EC873025.2|EC873025
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
EST: gi|211266105|gb|FL146506.1|FL146506
EST:     TGTTCTAGAGATACTAANGAACAATTCAAAGCTTGAAAGCGT-ATATGCT                         ATGACTGCTCATAGGGCTTTT
genomic: TGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAA-GCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTT
EST: gi|67012503|gb|CO441252.1|CO441252
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
EST: gi|211266094|gb|FL146495.1|FL146495
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTTCA-TTCTGTAA-CAGTATAAGAGAACA-C
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTT-CAATTCTGTAAACAGTATAAGAGAACAAC
EST: gi|149076177|gb|EE164770.2|EE164770
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCTATTCTGTAAACAGTAT
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTAT
EST: gi|211268534|gb|FL146513.1|FL146513
EST:     TGTTCTAGAGATACTAAGGAACAATTCAAAGGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGGCTTTTCAATTTCTGTAAACAGTATAAG
genomic: TGTTCTAGAGATACTAAGGAACAATTCAAAG-CTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGG-CTTTTCAATT-CTGTAAACAGTATAAG
EST: gi|101389305|gb|EB816607.1|EB816607
EST:     CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: CTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
EST: gi|32930116|gb|CF034928.1|CF034928
EST:     CGTTATATGCT                         ATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT
genomic: CGTTATATGCTgtaagctatt ... taatatgcagATGACTGCTCATAGGGCTTTTCAATTCTGTAAACAGTATAAGAGAACAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAAGAGGTTGTAACTCCATGGTTTAAGTTCCTCTGGGAGACATACAGGACTGTTCTAGAGATACTAAGGAACAATTCAAAGCTTGAAGCGTTATATGCTgtaagctattctcttatgagcattttgttgcttgcttctgttgaatttactttgtatgtggcacataaattttccatggtattggtacaacacattacca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC