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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaatatctttggtgtgtctatgtggatcaaaagtaagtatatgtgctatataccatcttgctaatgctgttcatgcaacccctggctcgtttggcgtgccaactcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCAAACGAAGAGGAGGATAGCGGCCGTGAGGACGCAGAGGAGGACCAGGCGT

Basic information

species Zea mays
transcript GRMZM2G107807_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|211017612|gb|FL417337.1|FL417337
EST:     AATCAAAAGCCCCCAACG-CAGCAGCAAAAGCAGCAAATCTAACTCTAAN                         CCATCAAAACAGATTCA-TTCTAACAGTAAGCCTGTG
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGAT-CAATTCTAACAGTAAGCCTGTG
EST: gi|60342404|gb|DN209377.1|DN209377
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|71449245|gb|DR830295.1|DR830295
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|211259582|gb|FL073576.1|FL073576
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|211262010|gb|FL073578.1|FL073578
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|47962533|gb|CN845242.1|CN845242
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|211481948|gb|FL389371.1|FL389371
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATT
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATT
EST: gi|78104107|gb|DV522525.1|DV522525
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|76285556|gb|DV025124.1|DV025124
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|211029321|gb|FL480588.1|FL480588
EST:     CCCCCTAGAAAAACAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: -CCCC--------CAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|60394653|gb|DN227523.1|DN227523
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|71763520|gb|DR961457.1|DR961457
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|32921335|gb|CF026147.1|CF026147
EST:     AATCAAAAGCCCCCAATGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|76285557|gb|DV025125.1|DV025125
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|211123592|gb|FL454334.1|FL454334
EST:     AATCAAARGCCCCCAACGGCAGCWGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACRGWTCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|5847293|gb|AW000372.1|AW000372
EST:     CCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: CCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|71444897|gb|DR825947.1|DR825947
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|60394161|gb|DN227031.1|DN227031
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|60351249|gb|DN218222.1|DN218222
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|211262011|gb|FL073579.1|FL073579
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|71433177|gb|DR814227.1|DR814227
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|31558778|gb|CD527990.1|CD527990
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|5525573|gb|AI861466.1|AI861466
EST:     AATCAAAAGCCCCCATCGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAANCAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|31558777|gb|CD527989.1|CD527989
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|91873364|gb|EB403321.1|EB403321
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|91055582|gb|EB166000.1|EB166000
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|45847164|gb|CN071107.1|CN071107
EST:     GCAGCAAAAGCAGCAAATCTAACTCTAAG                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: GCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
EST: gi|22714717|gb|BU197516.1|BU197516
EST:     AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAA                         CCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA
genomic: AATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 567

TAATAACCTGCCCACTGTTTATGAAGTTGTGACCGGGGTTGCTAAGAAGCAATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCAAACGAAGAGGAGGATAGCGGCCGTGAGGACGCAGAGGAGGACCAGGCGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 96

TAATAACCTGCCCACTGTTTATGAAGTTGTGACCGGGGTTGCTAAGAAGCAATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCAAACGAAGAGGAGGATAGCGGCCGTGAGGACGCAGAGGAGGACCAGGCGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 172

TAATAACCTGCCCACTGTTTATGAAGTTGTGACCGGGGTTGCTAAGAAGCAATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCAAACGAAGAGGAGGATAGCGGCCGTGAGGACGCAGAGGAGGACCAGGCGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

TAATAACCTGCCCACTGTTTATGAAGTTGTGACCGGGGTTGCTAAGAAGCAATCAAAAGCCCCCAACGGCAGCAGCAAAAGCAGCAAATCTAACTCTAAAgtaagtaaat ... actcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCAAACGAAGAGGAGGATAGCGGCCGTGAGGACGCAGAGGAGGACCAGGCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgctaatgctgttcatgcaacccctggctcgtttggcgtgccaactcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCAAACGAAGAGGAGGATAGCGGCCGTGAGGACGCAGAGGAGGACCAGGCGT
  tgctaat  putative branch site (score: 125)
                                              ctcttgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaatatctttggtgtgtctatgtggatcaaaagtaagtatatgtgctatataccatcttgctaatgctgttcatgcaacccctggctcgtttggcgtgccaactcttgcagCCATCAAAACAGATCAATTCTAACAGTAAGCCTGTGAAGCCAGCCCACCCAAACGAAGAGGAGGATAGCGGCCGTGAGGACGCAGAGGAGGACCAGGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA