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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggcttgctcttcgatataagaaaaacaagcaaatacaaaaaaaaagggaaagaactgaaacattagctaacatttttggcttcgtcgtcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTCTCTCCGCGCGGTGCAAGAACGGTATATGAACTCTGATAAAGATGTTCCC

Basic information

species Zea mays
transcript AC217975.3_FGT001
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217975.3_FGT001 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g44330.1 (Oryza sativa), 3'ss of exon 4
-attggcttgctcttcgatataagaaaaacaagcaaatacaaaaaaaaagggaaagaactgaaacatta----gctaacatttttggcttcgtcgtcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTCTCTCCGCGCGGTGCAAGAACGGTATATGAACTCTGATAAAGATGTTCCC
 | |   ||  | |  || ||||      |  |   ||     |         ||    ||  | | ||    | ||||   |||  | | ||    || |||||||| ||  ||| ||| ||||| || ||| ||||||||||||||||||||||  | || || || || ||||| |||||||| || |||||||||||||| 
gacta--ttcttataagacataatttgttcggggtcatcttttactgcctactaaattttggcatactaatgtgttaactcctttaaccttgta---aactgcagATATGTTTCATCACATCTACATCTCATGCTATTTGAATTGGTGAAGAACTCCTTGCGTGCAGTACAGGAACGATATATGAATTCCGATAAAGATGTTCCT
















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|148949845|gb|EC895336.2|EC895336
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32926546|gb|CF031358.1|CF031358
EST:     GGATCAGCTCCTGATATTACCATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32925671|gb|CF030483.1|CF030483
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTGCACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32926626|gb|CF031438.1|CF031438
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|76915117|gb|DV165832.1|DV165832
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|76292667|gb|DV032235.1|DV032235
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32926867|gb|CF031679.1|CF031679
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32925696|gb|CF030508.1|CF030508
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|148943884|gb|EC888964.2|EC888964
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32925393|gb|CF030205.1|CF030205
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32926562|gb|CF031374.1|CF031374
EST:     GGATCAGCTCCTGATATTACCATTTATGGCGATCCAAATTTTCCATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|13515941|gb|BG518217.1|BG518217
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32926448|gb|CF031260.1|CF031260
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32926835|gb|CF031647.1|CF031647
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|91055986|gb|EB166404.1|EB166404
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAA
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAA
EST: gi|32926291|gb|CF031103.1|CF031103
EST:     AGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32925566|gb|CF030378.1|CF030378
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32925964|gb|CF030776.1|CF030776
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32925456|gb|CF030268.1|CF030268
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|149112845|gb|EE295659.2|EE295659
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCC                         ATACGTCACATTACACCTACCCCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32925466|gb|CF030278.1|CF030278
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32925294|gb|CF030106.1|CF030106
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
EST: gi|32926657|gb|CF031469.1|CF031469
EST:     GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACATTTCC                         ATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC
genomic: GGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 8

TGGCTCAAGCTGCTTGTGAAGATGCCCGTTCTGTCTGTTTAAGGGAATATGGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTCTCTCCGCGCGGTGCAAGAACGGTATATGAACTCTGATAAAGATGTTCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 45

TGGCTCAAGCTGCTTGTGAAGATGCCCGTTCTGTCTGTTTAAGGGAATATGGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTCTCTCCGCGCGGTGCAAGAACGGTATATGAACTCTGATAAAGATGTTCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

TGGCTCAAGCTGCTTGTGAAGATGCCCGTTCTGTCTGTTTAAGGGAATATGGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTCTCTCCGCGCGGTGCAAGAACGGTATATGAACTCTGATAAAGATGTTCCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 59

TGGCTCAAGCTGCTTGTGAAGATGCCCGTTCTGTCTGTTTAAGGGAATATGGATCAGCTCCTGATATTAACATTTATGGCGATCCAAATTTTACGTTTCCgtaagttcca ... tcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTCTCTCCGCGCGGTGCAAGAACGGTATATGAACTCTGATAAAGATGTTCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagggaaagaactgaaacattagctaacatttttggcttcgtcgtcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTCTCTCCGCGCGGTGCAAGAACGGTATATGAACTCTGATAAAGATGTTCCC
                      agctaac  putative branch site (score: 59)
                         taacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggcttgctcttcgatataagaaaaacaagcaaatacaaaaaaaaagggaaagaactgaaacattagctaacatttttggcttcgtcgtcaaatgcagATACGTCACATTACACCTACACCTGATGTTATTTGAATTGGTGAAGAACTCTCTCCGCGCGGTGCAAGAACGGTATATGAACTCTGATAAAGATGTTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- -ggcttgc
- - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - caagcaa
- - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aactgaa