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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttctatcttttctctttggcatggtttcttttttaatccaacagattatattttaaatggtaatttgttgtacttgctgagcaaagcattttgg...

Basic information

species Zea mays
transcript GRMZM2G315931_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315931_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os08g37950.1 (Oryza sativa), 5'ss of exon 16
CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttctatcttttctctttggcatggtttcttttttaatcca-acagattatattttaaatggtaatttgttgtacttgctgagcaaagcattttgg
||| | ||||||||||||||||||||||||||||||| ||| |||||||||||||||||||||||||| ||||| |||||||||||||||  | | ||  ||||| | |   ||||      | | | |   |||      ||  |   ||||   ||  || | |  |  |   | |    
CTTGTTGATGCTTTAGAGTTGAGTAAAGAGACCATGAGGACAGTGAAGCAAAATCTTTGGTGGGCTTTTCTGTACAACATTgtatggttccctttctta-ctttgtcttctcttctccacggaacaatatgcattcagcaatatgtacaaattgtgtggcctagataggttatcaactaatc

upper sequence: GRMZM2G315931_T02 (Zea mays), 5'ss of exon 16
lower sequence: AT4G33520.3 (Arabidopsis thaliana), 5'ss of exon 16
CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatg--gttctatcttttctctttggcatggtttcttttttaatccaaca-gattatatt-ttaaatggtaatttgttgtacttgctg-agcaaagcattttgg
 |  | |||||  | ||| | |||    | ||||||||||| ||||||||||| ||||||||||| |||   || ||||||||| |  |||||   |||||   |    ||   ||  |||    | ||    || |||||  |||  |  |||| | || |  ||     | | | | |  | | 
TTGCTTGATGCGATGGAGCTAAGTCGGCAAACCATGAAGACCGTGAAGCAAAACCTTTGGTGGGCGTTCGGATACAACATTGTAAgttgttctgcattttcatgtcttaatttcttgctttgagtttcagtgtgaatatataattagttaataatgtattttgtttaaaatacctatgtaggtag-

upper sequence: GRMZM2G315931_T02 (Zea mays), 5'ss of exon 16
lower sequence: AT4G33520.2 (Arabidopsis thaliana), 5'ss of exon 16
CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatg--gttctatcttttctctttggcatggtttcttttttaatccaaca-gattatatt-ttaaatggtaatttgttgtacttgctgagcaaagcattttgg
 |  | |||||  | ||| | |||    | ||||||||||| ||||||||||| ||||||||||| |||   || ||||||||| |  |||||   |||||   |    ||   ||  |||    | ||    || |||||  |||  |  |||| | ||    ||| | |  | | |  | | |
TTGCTTGATGCGATGGAGCTAAGTCGGCAAACCATGAAGACCGTGAAGCAAAACCTTTGGTGGGCGTTCGGATACAACATTgtaagttgttctgcattttcatgtcttaatttcttgctttgagtttcagtgtgaatatataattagttaataatgtatt----ttgtttaaaatacctatgtag

upper sequence: GRMZM2G315931_T02 (Zea mays), 5'ss of exon 16
lower sequence: Vv12s0142g00330.t01 (Vitis vinifera), 5'ss of exon 8
CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttctatcttttctctttggcatg----gtttcttttttaatccaacagattatattttaaatggta----atttgttgta-cttgctgagcaaagcattttgg
 |  | |||||||| ||  | || | |   ||||||||||| ||||| ||||||||||||||||| ||    ||||||||||||  ||||| |     |      | ||      ||||||||||       || |     ||||||  ||||    |||||||||| |||||       | | ||||| 
TTGCTTGATGCTTTCGAACTAAGCAGACTAACCATGAAGACCGTGAAACAAAATCTTTGGTGGGCCTTTGCATATAACATTgta-agttcttttgcaacatacaagtatattgcatttcttttttttatgcccaaacctatttttaagaggtagagaatttgttgtaacttgc-------aaccttttg-

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|211170369|gb|FL103278.1|FL103278
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTATATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|60395664|gb|DN228534.1|DN228534
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTATATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|33094915|gb|CF054909.1|CF054909
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|78104271|gb|DV522689.1|DV522689
EST:     CATGAAGACGGTGAAGCAAAATCTTTGGGTGGCCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CATGAAGACGGTGAAGCAAAATCTTTGG-TGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|211347510|gb|FL460342.1|FL460342
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTATATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|67017000|gb|CO445749.1|CO445749
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTATATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|50324563|gb|CO519689.1|CO519689
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|86471147|gb|DY237517.1|DY237517
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGAGGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|50324564|gb|CO519690.1|CO519690
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|13249696|gb|BG360601.1|BG360601
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|60397501|gb|DN230317.1|DN230317
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|211347512|gb|FL460344.1|FL460344
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTATATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|12968157|gb|BG265104.1|BG265104
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|12968156|gb|BG265103.1|BG265103
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|89247265|gb|DY619051.1|DY619051
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGAGGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|211170365|gb|FL103274.1|FL103274
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|211347511|gb|FL460343.1|FL460343
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTATATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|211170368|gb|FL103277.1|FL103277
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
EST: gi|110518276|gb|EE022863.1|EE022863
EST:     CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATT                         GTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA
genomic: CCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttct ... tactctgcagGTTGGACTACCCATTGCTGCTGGAGCATTGCTTCCAGCTACGGGGACGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTATCGATGCTTTAGAGTTGAGTAAAGAGACCATGAAGACGGTGAAGCAAAATCTTTGGTGGGCTTTCCTGTATAACATTgtatggttctatcttttctctttggcatggtttcttttttaatccaacagattatattttaaatggtaatttgttgtacttgctgagcaaagcattttgg

- - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG