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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaataatgtttgttattctctatctttgagaatatgaatactgtcgaatccgtatgctggcaaacaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG

Basic information

species Zea mays
transcript GRMZM2G043198_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 4
aacaataatgtttgttattctctatctttgagaatatgaatactgtcgaatccgtatgctggcaa----acaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
  || |    |   |   |||  |||||| | |  |   ||| | ||  |||  |||| ||  ||    | ||   | |  ||  ||||||||   || ||||||||||||||||||| || ||||||||||||||||||||||||||||| ||||| ||||||   ||||||||||| ||||| || ||||| ||||||||||
ttcacttccatgcata--tctggatcttttata-caaatatattttcccatctatatgatgtaaagattaaaatagtttctataacaccatttgc-atattcagGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG

upper sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 6
aacaataatgtttgttatt---ctctatctttgaga-atatgaatactgtcgaatccgtatgctggcaaacaaatctcttaatt-gcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
   |||  |||||  | ||   ||  || ||   || |||  | | |  ||   |   | |  | || | || ||   ||| |  |    |   ||| | | |||||||| ||||| || ||||| || || || || || |||||||||||||||||||| |||||||| |||||||||||||| || || |||||||| ||||
---aatggtgtttagttttgggcttcattttattgatataccactgc-atcatcttgatttattagctagcagattaattattcagttttaacctttgt-tgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG

upper sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 6
aacaataatgtttgttattctctatctttgag-aatatg-aatactgtcgaatccgtatgctggcaaacaaatctcttaatt-gcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
   |||  ||||| || |   ||   ||||    ||||| |      ||   | | | |  |||| | |  ||   ||| |  |    |   ||| | | |||||||| ||||| || ||||| || || || || || |||||||||||||||||||| ||||| || |||||||||||||| || || |||||||||||||
--taatggtgtttattttgggcttcatttgtttgatatgcagctacatcatcttcatttattggctagcggattaattactcagttttaacctttgt-tgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG

upper sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 6
---aacaataatgtttgttattctctatctttgagaata--tgaatactgtcgaatccgtatgctggcaaacaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
        | |  ||||  ||||  |   ||     | |  |||||  | |  ||    |  ||| ||| |  |||   ||| ||  | | ||| ||     |||||||| ||||| || ||||| || || || || || |||||||||||||||||||| |||||||| |||||||||||||| || || |||||||||||||
aatggtgtttagttttgggattcatttgtttgatatacagctgaatcatctt-aacttattagctagcagattaattatttagttttaacctttgttg----cagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG

upper sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
aacaataatgtttgttattctctatctttgagaatatgaatactgtcgaatccgtat-gctggcaaacaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
  || | ||  |     || |||   || |   ||   | | |  |  | | |  ||   |  | ||    | || ||||       |  | |   |||||||||||||||| || || ||||| ||||| ||||| || |||||||||||||| ||||||  ||| || || |||||||| || || |||||||||||||
tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaat-atctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG

upper sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 3'ss of exon 7
----aacaataatgtttgtt-attctctatctttg-agaatatgaatactgtcgaatccgtatgctggcaaaca-aatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
     |   |  | | || | |   | | | |||| |  |  |    | ||| | |||  | |  |||  || |  ||||| |  ||| |    ||||| ||  ||||||||||| ||||| |||||||| ||||| || || ||||||||||| ||||| |||||||| || |||||||| ||||| || |||||||||||||| |
gacctaatttggtatatgatgaaaatgtgtttttgtattacttcttcattgtaggatctct-ttttggtgaatatgatctcatttttgga----tttttttg--cagGCAATTGACCACATCATTAATTCTGCTGCAAAATCAAACTACATGTCCGCTGGTCAGATATCCGTACCTATTGTTTTTAGAGGACCAAATGGTGCTGCCG

upper sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
aacaataatgtttgttattctctatctttgagaatatgaatactgtcgaatccgtatgctggcaaacaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
    ||   ||| || |   | |   |||       | ||   | |    |   | |  |          | | |||||  ||| |||   |   | ||||||||||| || ||||||||||||||||| ||||| ||||| ||||||||||| ||||||||||| || ||||| || || || |||||||| |||||||
gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG

upper sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
lower sequence: EFJ19158 (Selaginella moellendorffii), 3'ss of exon 4
aacaataatgtttgttattctctatctttgagaatatgaatactgtcgaatccgtatgctggcaaacaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
                                                 || | |||  ||   |     | |  ||| |        |  |   || |||| ||||||||||| || || || || || ||| |  |||| ||||| |  ||||| ||||||||||| ||||| ||| ||||||| |||||||| ||||
---------------------------------------------gtagatgcttatcatgtttacgtttttttctaagtcttgttcgtggtgattttagGCTATTGATCACATCATCAACTCTGCAGCAAAGACATACTATATGTCCGGAGGGCAAATATCTGTTCCCATTGTATTTCGGGGTCCCAATGGTGCAGCTG

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|211444057|gb|FL415432.1|FL415432
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCG
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCG
EST: gi|211491514|gb|FL426447.1|FL426447
EST:     ATGGTCTTCGAC-TATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTGATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211003333|gb|FL404181.1|FL404181
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTC
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTC
EST: gi|148930818|gb|EC873192.2|EC873192
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211084499|gb|FL378037.1|FL378037
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACA
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACA
EST: gi|32828890|gb|CD968568.1|CD968568
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|38687965|gb|CK144996.1|CK144996
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: -TGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|93281968|gb|EB674232.1|EB674232
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211311674|gb|FL419261.1|FL419261
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211503999|gb|FL380203.1|FL380203
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211395332|gb|FL395257.1|FL395257
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211017664|gb|FL418154.1|FL418154
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTGTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211499368|gb|FL394923.1|FL394923
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211063939|gb|FL426137.1|FL426137
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCNAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|32828953|gb|CD968631.1|CD968631
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211542664|gb|FL412592.1|FL412592
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTWATTYAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211479962|gb|FL426376.1|FL426376
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|31357689|gb|CD442046.1|CD442046
EST:     ATGGGCTTCGACCTATTGGAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
EST: gi|211016844|gb|FL388973.1|FL388973
EST:     ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAG                         GCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT
genomic: ATGGTCTTCGACCTATTGTAGAGTTCATGACATTTAACTTTTCGATGCAGgtcagatgtt ... ttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaatccgtatgctggcaaacaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG
                           tcttaat  putative branch site (score: 3)
                                      ccatttttt  putative PPT
                                        attttttatgttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaataatgtttgttattctctatctttgagaatatgaatactgtcgaatccgtatgctggcaaacaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT