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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtcttctagtatcattctgctttattccgtgctaagttcttgtggtaagaagctaagcactttaaatcagttgacggtttctcgaaataattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATGGATAAGAAGAAAGGGACCGATGGCACCGAACCAGGACCAGCTCCATCTC

Basic information

species Zea mays
transcript GRMZM2G047223_T03
intron # 1
splice site 3'
intron type U2

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|211224492|gb|FL322782.1|FL322782
EST:     CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211316770|gb|FL360982.1|FL360982
EST:     CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACMAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|78113905|gb|DV532294.1|DV532294
EST:     CTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211004390|gb|FL335892.1|FL335892
EST:     CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211322760|gb|FL352838.1|FL352838
EST:     TCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCG-C-CGCGATGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGAT
genomic: TCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGA-GAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGAT
EST: gi|211312819|gb|FL367452.1|FL367452
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGRG-GAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211078309|gb|FL342738.1|FL342738
EST:     CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211402149|gb|FL346428.1|FL346428
EST:     CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211274707|gb|FL354611.1|FL354611
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211199995|gb|FL308017.1|FL308017
EST:     CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGA-TTCGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211463075|gb|FL352967.1|FL352967
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAYGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGAT
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTA-GGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGAT
EST: gi|211107631|gb|FL307913.1|FL307913
EST:     CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|91877110|gb|EB407067.1|EB407067
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|89758012|gb|DY687355.1|DY687355
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211419360|gb|FL322265.1|FL322265
EST:     CCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGA-TTCGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|89756849|gb|DY686713.1|DY686713
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|91874336|gb|EB404293.1|EB404293
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211241359|gb|FL313117.1|FL313117
EST:     GAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGA-TTCGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: GAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211342758|gb|FL350527.1|FL350527
EST:     CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|78117555|gb|DV535942.1|DV535942
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|71771758|gb|DR969695.1|DR969695
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|78118515|gb|DV536899.1|DV536899
EST:     CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CTCCTCCCCTCCTCCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
EST: gi|211258118|gb|FL346785.1|FL346785
EST:     CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAG                         GATATCGA-TTCGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG
genomic: CCCGAGATCCGGGCAAAGCGCGCCGCGCGAGAACCAGgtcggtcatc ... taattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtaagaagctaagcactttaaatcagttgacggtttctcgaaataattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATGGATAAGAAGAAAGGGACCGATGGCACCGAACCAGGACCAGCTCCATCTC
                          agttgac  putative branch site (score: 4)
                                          aaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtcttctagtatcattctgctttattccgtgctaagttcttgtggtaagaagctaagcactttaaatcagttgacggtttctcgaaataattggcagGATATCGATTTAGGTATATGGACAAGGTGTCTGAAGGTACTAAGTGAGATGGATAAGAAGAAAGGGACCGATGGCACCGAACCAGGACCAGCTCCATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC