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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagcgttcttgtagcaaaatcttttactttctattccatactatatttttcctgtagaattctaatgtactcctttttttactataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA

Basic information

species Zea mays
transcript GRMZM2G085670_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085670_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
gaagcgttcttgtagcaaaatcttttactttcta-ttccatactatatttttcctgtag--aattctaa-tgtactcctttttttactataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA
     |||| ||||| |  ||||||||| ||  |  ||  | |||| ||||| || |||  ||| |||| ||| ||   ||||| | ||| |||| |  ||||| | |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| || ||||||||||||||||| || 
--caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggttttt-attatcatttcta-ttcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG

upper sequence: GRMZM2G085670_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
-gaagcgttcttgtagcaaaatcttttactttctattccatactatatttttcctgtagaattctaatgtactcctttttttactata-attttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA
   |   || || |  | |  |   || |     |||||  | |||     |  || | | ||  |   |  ||  |   | | | |   ||  ||   ||| |||| || |||||||| || ||||| || || |||||| | || ||| | ||||| ||||||||||| |||||||||||||||||| | 
tccattttttttttttccattttgcttccaccaaattcctgattatgacagt--tgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
















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|101398140|gb|EB820944.1|EB820944
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|93013201|gb|EB638721.1|EB638721
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|50325881|gb|CO521007.1|CO521007
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|101390708|gb|EB817288.1|EB817288
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|32927905|gb|CF032717.1|CF032717
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|71330909|gb|DR802251.1|DR802251
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211281967|gb|FL132368.1|FL132368
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGWGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211512613|gb|FL228206.1|FL228206
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|32927110|gb|CF031922.1|CF031922
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211512616|gb|FL228209.1|FL228209
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACYCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211512615|gb|FL228208.1|FL228208
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|74236689|gb|DT644603.1|DT644603
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|32927326|gb|CF032138.1|CF032138
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|76936648|gb|DV174824.1|DV174824
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211512612|gb|FL228205.1|FL228205
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211512608|gb|FL228201.1|FL228201
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|76294401|gb|DV033969.1|DV033969
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211512617|gb|FL228210.1|FL228210
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTT
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTT
EST: gi|89247571|gb|DY619357.1|DY619357
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|32928013|gb|CF032825.1|CF032825
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211281965|gb|FL132366.1|FL132366
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACG
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACG
EST: gi|71423346|gb|DR806010.1|DR806010
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|32927322|gb|CF032134.1|CF032134
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211512610|gb|FL228203.1|FL228203
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|211514961|gb|FL228214.1|FL228214
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
EST: gi|32927333|gb|CF032145.1|CF032145
EST:     TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA
genomic: TCCGAAAGCTAAAGCAACTCAGTGTGCTAACTCTGGCAGAGTCAACTAAGgtacgaattc ... ttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttcctgtagaattctaatgtactcctttttttactataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA
               ttctaat  putative branch site (score: 2)
                         ctcctttttttactat  putative PPT
                             tttttttactataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagcgttcttgtagcaaaatcttttactttctattccatactatatttttcctgtagaattctaatgtactcctttttttactataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA