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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggtttcttgaattttcatgtactatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA

Basic information

species Zea mays
transcript GRMZM2G114911_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114911_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g45180.1 (Oryza sativa), 3'ss of exon 1
-tttggtttcttgaattttcatgtac-tatctattaaacatttctcta-agcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA
  |    |  ||| |||||| |   | | ||| |  | |||      | | | ||  ||||||   |   |   |    | ||||   |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| |||||||
actattctctttgcattttcgttagcatttctctatagcatcggatgatacctaccgtgtccaatgatttcccacttaatcgaat---aatcttatgtttcagATCACATACCACTTTTTCCATTGGAAGAAGGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAGCAAATGGACAATGGCA

upper sequence: GRMZM2G114911_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G02540.1 (Glycine max), 3'ss of exon 1
---------tttggtttcttgaattttcatgtactatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA
          ||  | | |||  |||  |  || | | || |  |  ||    |||   |  || || | ||  | |||      | || | ||  |  | |   |||| | ||||| |||||||| || |||||||||||||| || ||||| || ||||| || || |||||   ||||||||||||||||||  | || ||||| |
aggttataaattaatattttg--tttgtaaatattgt-taatggatgttaaaataatttaacttctctacatggcgctta----attgattatg--ttgtgtccatcagGTAACATATCACTTTTTTCACTGGAAGAAAGGAACTCCATTTGCGGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: GRMZM2G114911_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G05940.1 (Glycine max), 3'ss of exon 1
--tttggtttcttgaattttcatgtactatctatta--aacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA
    |  |   || |  | |  | |   |  ||||   ||    |    || ||| ||        |||   | |||   | || | ||  |  | |   |||| | ||||| |||||||| || |||||||||||||| || ||||| || ||||| || || |||||   ||||||||||||||||||  | || ||||| |
caggttataaattaatctgttgtttgtaaattattgttaatggatgctaaaacaatttaacttctctaaa--tggcctaattgattatg--ttgtgtccatcagGTAACATATCACTTTTTTCACTGGAAGAAAGGAACTCCATTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: GRMZM2G114911_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G01830.1 (Glycine max), 3'ss of exon 1
tttggtttc---ttgaattttcatgtacta-tctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA
|  ||||     || |  |||  | |   | | |  | ||    | |  ||  || |||  |      ||| | ||    | || | ||  |  | |   |||| | |||||  ||||||| || |||||||||||||| || ||||| || ||||| || || |||||   ||||||||||||||||||  | || ||||| |
tcaggttataaattaatattttgtttgtaaatattgttaatggatgttaaaataa-tttaacttctctaca-tggcttaattgattatg--ttgtgtccatcagGTAACATATGACTTTTTTCACTGGAAGAAAGGAACTCCGTTTGCAGAGGACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAA

upper sequence: GRMZM2G114911_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
tttggtttcttgaattttcatgtactatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA
           | ||| |     |    ||   |  || ||    ||       | || ||||     |||   | | || | |   | || ||||  || |||| || || |  |||||||||||||| |||||||| ||||  ||||| || ||| | || ||   ||||||||||||||| || || ||||||||||
-----------gtattattcccgatctcctccgatccaatttcgaaattgttggtttctagat-----ttgaatttttgagttt---ttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA

upper sequence: GRMZM2G114911_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G01230.1 (Arabidopsis thaliana), 3'ss of exon 1
tttggtttcttgaattttcatgtactatctattaaacatttctctaagcaa-ctttgtccagataacacttgccatctggaat--gtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA
 | |  ||  |  ||| |||   || |  | |||| |   | |||||  |  ||||    | ||   |  |   |   | |||  ||| || ||  || |||| | || || |||   ||||| |||| ||||||||| |||||||| |||||||| ||||| ||||| |  || ||||||||||| |||||||| |||||  
-tggcattgcttgattgtca-aaaccaaat-ttaatctaatttctaattactctttaggaaaatgtgatgtctgagtagaaatttgtggatatttgttgtcagGTAACGTATCACAGCTTCCACTGGATGAAAGGAACTCCTTTTGCAGATGACCAAGGAATCTACAATGGTTTAACTTGGTGGGAACAAATGGACAATGGTC

upper sequence: GRMZM2G114911_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0046g00140.t01 (Vitis vinifera), 3'ss of exon 1
tttggtttcttgaattttcatgtactatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA
 || |||| |    |||   ||||    ||     |   | |  ||    ||||| |         |    |    ||    |      | |   || || |||| || ||||| |||||||||||||||||||| ||||||||||| ||||||||||| |||||    ||||| ||||||||||| || || ||||| |
gtttgtttatcttctttgtctgtatacccttcctgatgctacattagattactttatatcctctctatgacctgattgaggagcatgcttcacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGACCAGGGAATCTACAATAGGTTGACGTGGTGGGAGCAGATAGACAATGGAA

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|71445807|gb|DR826857.1|DR826857
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|211416728|gb|FL206619.1|FL206619
EST:     CTGCACCCCTGGCACCGCGTGGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTT
genomic: CTGCACCCCTGGCACCGCGTGG-ACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTT
EST: gi|78082275|gb|DV510687.1|DV510687
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|32907378|gb|CF012191.1|CF012191
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|78081154|gb|DV509566.1|DV509566
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|6681814|gb|AW287801.1|AW287801
EST:     GACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|94474062|gb|EB703020.1|EB703020
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTTCACTTCGCG                         ATCACTTACCACTTTTT
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTT
EST: gi|211414178|gb|FL206607.1|FL206607
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|78082274|gb|DV510686.1|DV510686
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|211453252|gb|FL452574.1|FL452574
EST:     CGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: CGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|78081153|gb|DV509565.1|DV509565
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|71445808|gb|DR826858.1|DR826858
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|211416727|gb|FL206618.1|FL206618
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCA
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCA
EST: gi|211414185|gb|FL206614.1|FL206614
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|32823856|gb|CD963578.1|CD963578
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|60397481|gb|DN230297.1|DN230297
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|211414180|gb|FL206609.1|FL206609
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGAC
EST: gi|211414177|gb|FL206606.1|FL206606
EST:     GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCG                         ATCACATACCACTTTTTCCATTGGAAGAA
genomic: GCTGCACCCCTGGCACCGCGTGGACCGTCGTCAACCTCTTCCACTTCGCGgtaaccgcct ... tatttttcagATCACATACCACTTTTTCCATTGGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA
              agataac  putative branch site (score: 3)
                                          tcttatttttc  putative PPT
                                      tgaatcttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggtttcttgaattttcatgtactatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttatttttcagATCACATACCACTTTTTCCATTGGAAGAAAGGAACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAGCAAATGGATAATGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA