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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttccctgtaattaatgctttgataccttaagtttgctgagctttgcacgggttcttcgatgttcttttgttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG

Basic information

species Zea mays
transcript GRMZM2G055276_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055276_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 4
gttagtttccctgtaattaatgctttgataccttaagtttgctgagctttgcacgggttcttcgatgt-tcttttgttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG
||   |||| | ||      |  ||  || |||  ||||  ||||   | | |    || ||   |   | |    || |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
gtatatttctcagtgtgctctatttcaatccctacagttgtctgattctagaatttttttttgattaaatgtaccattttcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG
















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|29944931|gb|CB815382.1|CB815382
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|211203087|gb|FL446559.1|FL446559
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|211542473|gb|FL178318.1|FL178318
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|8103173|gb|AW927830.1|AW927830
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|24773994|gb|CA409248.1|CA409248
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATG
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATG
EST: gi|8930043|gb|BE224881.1|BE224881
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|24768909|gb|CA404038.1|CA404038
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|60338211|gb|DN205184.1|DN205184
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|32829108|gb|CD968786.1|CD968786
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|148956947|gb|EC902885.2|EC902885
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTTTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|32829065|gb|CD968743.1|CD968743
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGATCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|22542691|gb|BU093129.1|BU093129
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|60345377|gb|DN212350.1|DN212350
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|21331537|gb|BQ486918.1|BQ486918
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|18383516|gb|BM416716.1|BM416716
EST:     TGCAGCCACTTTCAACCAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|7238136|gb|AW573358.1|AW573358
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAGGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|60353592|gb|DN220565.1|DN220565
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|60339365|gb|DN206338.1|DN206338
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|60337216|gb|DN204189.1|DN204189
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|5152768|gb|AI759066.1|AI759066
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGNCAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|32829328|gb|CD969006.1|CD969006
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|113704047|gb|EE681551.1|EE681551
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|60349042|gb|DN216015.1|DN216015
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATACGAAGAAGGAAAATGTTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|31364091|gb|CD448446.1|CD448446
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGCCAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|32840679|gb|CD980360.1|CD980360
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTCTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|32840680|gb|CD980361.1|CD980361
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
EST: gi|30087789|gb|CB885995.1|CB885995
EST:     TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTG                         GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC
genomic: TGCAGCCACTTTCAAACAAGAAAGAAAATGATGAAGTTTTCATTAAGCTGgttagtttcc ... gttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttaagtttgctgagctttgcacgggttcttcgatgttcttttgttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG
                                    tgttcttttgttctct  CT-rich tract
                                      ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttccctgtaattaatgctttgataccttaagtttgctgagctttgcacgggttcttcgatgttcttttgttctcttagGGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGTGATGAGCGTGCCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG