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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtttagacactaatcatgctacccttcaatgttttcatcactgatgtttttctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAGGATGAAGATGATGAGAGCGGTGAAGAGTATGAAGAAGAGGAAGAGCGTG

Basic information

species Zea mays
transcript GRMZM2G016817_T02
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|18963781|gb|BM660626.1|BM660626
EST:     AGAAGGAACCCAATAGTACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCAGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|78543891|gb|DV621389.1|DV621389
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|211218875|gb|FL461796.1|FL461796
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|69351460|gb|DR452142.1|DR452142
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|211447945|gb|FL055692.1|FL055692
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAA
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAA
EST: gi|26456563|gb|CA828146.1|CA828146
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|211443699|gb|FL055661.1|FL055661
EST:     AGAAGGAACCCAWTAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|20300963|gb|BQ163906.1|BQ163906
EST:     AGAAGGAACCCAATAGTACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCAGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTTAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|67015263|gb|CO444012.1|CO444012
EST:     AGAAGGAACCCAATAGTACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|211445823|gb|FL055680.1|FL055680
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCG
EST: gi|20301050|gb|BQ163993.1|BQ163993
EST:     AGAAGGAACCCAATAGTACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCAGAGTCTCATTTGAAGGCGACAA
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAA
EST: gi|211447939|gb|FL055686.1|FL055686
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACWAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|22542301|gb|BU092739.1|BU092739
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAG-GGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|20301540|gb|BQ164483.1|BQ164483
EST:     CCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: CCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|211445826|gb|FL055683.1|FL055683
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
EST: gi|60350291|gb|DN217264.1|DN217264
EST:     AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATG                         ACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG
genomic: AGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAG

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), 48 (downstream exon)
Score: 291

GCCCACAATATTTGAAGTAGCGACTGGGGTTGCCAAGAAACAAAACAAGGAGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAGGATGAAGATGATGAGAGCGGTGAAGAGTATGAAGAAGAGGAAGAGCGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 170

GCCCACAATATTTGAAGTAGCGACTGGGGTTGCCAAGAAACAAAACAAGGAGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAGGATGAAGATGATGAGAGCGGTGAAGAGTATGAAGAAGAGGAAGAGCGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 190

GCCCACAATATTTGAAGTAGCGACTGGGGTTGCCAAGAAACAAAACAAGGAGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAGGATGAAGATGATGAGAGCGGTGAAGAGTATGAAGAAGAGGAAGAGCGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GCCCACAATATTTGAAGTAGCGACTGGGGTTGCCAAGAAACAAAACAAGGAGAAGGAACCCAATAATACCAGCAAAAGCAACAAACCAAGTTCGAAAATGgtaaagttta ... tctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAGGATGAAGATGATGAGAGCGGTGAAGAGTATGAAGAAGAGGAAGAGCGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacactaatcatgctacccttcaatgttttcatcactgatgtttttctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAGGATGAAGATGATGAGAGCGGTGAAGAGTATGAAGAAGAGGAAGAGCGTG
                                       tgtttttctgtttc  CT-rich tract
                      aatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtttagacactaatcatgctacccttcaatgttttcatcactgatgtttttctgtttcagACAACAAGACCCGAGTCTCATTTGAAGGCGACAAAAGTGGCGCCCCCTAAGGATGAAGATGATGAGAGCGGTGAAGAGTATGAAGAAGAGGAAGAGCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA