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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatctcctatatcaatttagttgatccttaaccgccttcgttttgatttaatagatcagcagtctaggcaacttatagtgtgtgcattgttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAGGCATGTCCGTGATAGAGACAGGGGCTATCGTCGTCGGAGCAGAAGTAGA

Basic information

species Zea mays
transcript GRMZM2G016296_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016296_T06 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 5
---taatctcctatatcaatttagttgatccttaaccgccttcgttttgatttaatagatcagcagtctaggcaacttatagtgtgtgcattgttttaactagGCACAGAGAT------------AGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAGGCATGTCCGTGATAGAGACAGGGGCTATCGTCGTCGGAGCAGAAGTAGA
   || | |  |||| | || ||   |    || |     |  | ||| | | || |  | || || | | |  | |||| || | |  ||||||| ||  ||||||||||||            ||||| |  ||  ||| |||||||||||| |||||||||||||||| |||||| || || ||||   |||||||||              
acttagtatagtataactatctaagagtgattttatttgatctgatttcagtaaa-attttagtagcccatgggatttatggtattt--attgtttcaatcagGCACAGAGATGACCACAGAGATAGAGAACGCAGGGGCCGAAGTCGCAGCAGAAGCAGAGAAAGGCATGGCCGTGACAGGGATAGGGATCATCGTCGTCAC------------
















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|87157632|gb|DY402421.1|DY402421
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGACAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|33100209|gb|CF060169.1|CF060169
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|33100317|gb|CF060277.1|CF060277
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|18384287|gb|BM417486.1|BM417486
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|71766439|gb|DR964376.1|DR964376
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|33098747|gb|CF058707.1|CF058707
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|74235570|gb|DT643484.1|DT643484
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|71421374|gb|DR805394.1|DR805394
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|211456040|gb|FL150302.1|FL150302
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGACAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|211422683|gb|FL350037.1|FL350037
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|6022225|gb|AW067153.1|AW067153
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|32830771|gb|CD970449.1|CD970449
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|76280364|gb|DV019932.1|DV019932
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|71317634|gb|DR795571.1|DR795571
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|22489702|gb|BU049625.1|BU049625
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGGCAAG                         GCACAGAGATAGAGATCATAGAAGC
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGC
EST: gi|26558961|gb|CA831196.1|CA831196
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGACAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|33099574|gb|CF059534.1|CF059534
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|76936777|gb|DV174882.1|DV174882
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|50336916|gb|CO532042.1|CO532042
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|22545919|gb|BU098278.1|BU098278
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGACAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|74232258|gb|DT640172.1|DT640172
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|211456033|gb|FL150295.1|FL150295
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAKTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
EST: gi|211456029|gb|FL150291.1|FL150291
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAG
EST: gi|91873269|gb|EB403226.1|EB403226
EST:     GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAG                         GCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG
genomic: GGGGTTGAGAAATCACAAGACAGATCAAGAAGCCGCAGTCCAAGGCCAAGgtgaagactt ... ttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttaatagatcagcagtctaggcaacttatagtgtgtgcattgttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAGGCATGTCCGTGATAGAGACAGGGGCTATCGTCGTCGGAGCAGAAGTAGA
 atttaat  putative branch site (score: 4)
                                          ttgtttt  putative PPT
                                         attgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatctcctatatcaatttagttgatccttaaccgccttcgttttgatttaatagatcagcagtctaggcaacttatagtgtgtgcattgttttaactagGCACAGAGATAGAGATCATAGAAGCCAAAGTCGCAGCAGGAGCAGAGAAAGGCATGTCCGTGATAGAGACAGGGGCTATCGTCGTCGGAGCAGAAGTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT