Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttacatcctctttaaattagatacttaatatttgcataaaccattcctgtgagactcgtaaatgcgtcatttaccactaatggtagtattttttcttcttatttttagtggttttacattggtctttagtttctagtgttgcctaaagtatttttggcgtcatatccataatattatgcatgttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA

Basic information

species Zea mays
transcript GRMZM2G085670_T01
intron # 4
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|32927438|gb|CF032250.1|CF032250
EST:     ATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: ATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|50325881|gb|CO521007.1|CO521007
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|101390708|gb|EB817288.1|EB817288
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|32927905|gb|CF032717.1|CF032717
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|32927397|gb|CF032209.1|CF032209
EST:     ATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: ATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|71423346|gb|DR806010.1|DR806010
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|32927110|gb|CF031922.1|CF031922
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|71764777|gb|DR962714.1|DR962714
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|76936648|gb|DV174824.1|DV174824
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|211512615|gb|FL228208.1|FL228208
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|149000178|gb|EE037317.2|EE037317
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|32927326|gb|CF032138.1|CF032138
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|76294401|gb|DV033969.1|DV033969
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|211512612|gb|FL228205.1|FL228205
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|89247571|gb|DY619357.1|DY619357
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|32928013|gb|CF032825.1|CF032825
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGGCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|31360706|gb|CD445063.1|CD445063
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|32927322|gb|CF032134.1|CF032134
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|101398140|gb|EB820944.1|EB820944
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|78090434|gb|DV518808.1|DV518808
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|32927333|gb|CF032145.1|CF032145
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
EST: gi|78090435|gb|DV518809.1|DV518809
EST:     CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA                         GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
genomic: CCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA

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: 48 (upstream exon), 45 (downstream exon)
Score: 209

ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 113

ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 122

ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 128

ATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCAgtgagttgtt ... gttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcctaaagtatttttggcgtcatatccataatattatgcatgttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA
    gcctaaa  putative branch site (score: 128)
                         atatccataatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttacatcctctttaaattagatacttaatatttgcataaaccattcctgtgagactcgtaaatgcgtcatttaccactaatggtagtattttttcttcttatttttagtggttttacattggtctttagtttctagtgttgcctaaagtatttttggcgtcatatccataatattatgcatgttcatgtagGGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG