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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgcttggattccttctcgccaatcagtcaggacgcaagagttgtatgtagatcattaattttggtttgtctgtcttcgttcttgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGACGAGGCGAGGAGCTACGCCATCTGTAAGGCGGAGGAAGTGGAGCAAGAG

Basic information

species Zea mays
transcript GRMZM2G173321_T02
intron # 3
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|211138903|gb|FL206376.1|FL206376
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|26456740|gb|CA828323.1|CA828323
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|76936192|gb|DV174627.1|DV174627
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|78074656|gb|DV503090.1|DV503090
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|149051910|gb|EE156043.2|EE156043
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|78093455|gb|DV521829.1|DV521829
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|26457345|gb|CA828928.1|CA828928
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|211138901|gb|FL206374.1|FL206374
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTYACGCGACCC
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGT-ACGCGACC-
EST: gi|71333334|gb|DR803728.1|DR803728
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|60397540|gb|DN230356.1|DN230356
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|93281470|gb|EB673734.1|EB673734
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|211138904|gb|FL206377.1|FL206377
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|211138900|gb|FL206373.1|FL206373
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGG
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGG
EST: gi|211139833|gb|FL206379.1|FL206379
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|211139832|gb|FL206378.1|FL206378
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|211138902|gb|FL206375.1|FL206375
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|20507484|gb|BQ279652.1|BQ279652
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
EST: gi|71333335|gb|DR803729.1|DR803729
EST:     GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG                         GACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA
genomic: GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGA

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: 114

GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGACGAGGCGAGGAGCTACGCCATCTGTAAGGCGGAGGAAGTGGAGCAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 12

GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGACGAGGCGAGGAGCTACGCCATCTGTAAGGCGGAGGAAGTGGAGCAAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 21

GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGACGAGGCGAGGAGCTACGCCATCTGTAAGGCGGAGGAAGTGGAGCAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 16

GAGGTTCCAACTTTTTGGAGAAAGATTAGGAGgtacgcgctt ... tgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGACGAGGCGAGGAGCTACGCCATCTGTAAGGCGGAGGAAGTGGAGCAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttgtatgtagatcattaattttggtttgtctgtcttcgttcttgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGACGAGGCGAGGAGCTACGCCATCTGTAAGGCGGAGGAAGTGGAGCAAGAG
               cattaat  putative branch site (score: 16)
                               tctgtcttcgttctt  putative PPT
          tagatcattaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcgcttggattccttctcgccaatcagtcaggacgcaagagttgtatgtagatcattaattttggtttgtctgtcttcgttcttgagtggcagGACGTATGGATCAGTGAGAAAAGATCTGGAAAACCGGGTGTACGCGACCGACGAGGCGAGGAGCTACGCCATCTGTAAGGCGGAGGAAGTGGAGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA