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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacagtcttttcttttatattgtagtttttcgtctattaccttctattggcagtcaataccttttttgagttatgtttgcgtaatttatctttatcatgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG

Basic information

species Zea mays
transcript GRMZM2G484880_T04
intron # 5
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|76912438|gb|DV164732.1|DV164732
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
EST: gi|71434326|gb|DR815376.1|DR815376
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAAGAAACGTAAAAGTCCAGCTTGGGACTGAG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAA-GAAACGTAAAAGTC-AGCTTGGGACTGAG
EST: gi|6031476|gb|AW076378.1|AW076378
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
EST: gi|93284203|gb|EB676467.1|EB676467
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAAAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCCTGGG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGG
EST: gi|13178287|gb|BG349545.1|BG349545
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTA
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTA
EST: gi|211058547|gb|FK994412.1|FK994412
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
EST: gi|32913308|gb|CF018120.1|CF018120
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGCGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
EST: gi|26456042|gb|CA827625.1|CA827625
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
EST: gi|71438521|gb|DR819571.1|DR819571
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
EST: gi|166482492|gb|EG041825.1|EG041825
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGC
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGC
EST: gi|71331879|gb|DR802817.1|DR802817
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
EST: gi|32865668|gb|CF005350.1|CF005350
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
EST: gi|31997934|gb|CD661839.1|CD661839
EST:     CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCA                         TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGATT
genomic: CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGATT

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: 39 (upstream exon), 44 (downstream exon)
Score: 287

CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG


Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 133

CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG


Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 162

CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG


Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 132

CGGATGCAAAAGCTGATAAAGATGACACTAAGAGTCTCAgtgagtacag ... catgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtcaataccttttttgagttatgtttgcgtaatttatctttatcatgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG
                                      tctttatc  CT-rich tract
                               taatttatctttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacagtcttttcttttatattgtagtttttcgtctattaccttctattggcagtcaataccttttttgagttatgtttgcgtaatttatctttatcatgtttaagTTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT