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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatcatatgtactataccacaatatctactccctccaatatttgtattgttacttataatctctaacaaagtttttcacgtttcaatttcccacctgcag

Basic information

species Zea mays
transcript GRMZM2G116919_T01
intron # 3
splice site 5'
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|37421879|gb|CF648643.1|CF648643
EST:     ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAG                         GTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
genomic: ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
EST: gi|76917612|gb|DV166918.1|DV166918
EST:     AAGGCACACCCTTTGAAGG                         GGGGATATT-CTATGGGGAAACTCAAATTTCCACCGGATTATCCTTTTTA
genomic: AAGGCACACCCTTTGAA-Ggtaaagatca ... ccacctgcagGTGGATATTACTAT-GGGAAACTCAAATTTCCACCGGATTATCC-TTTTA
EST: gi|31364477|gb|CD448832.1|CD448832
EST:     ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAG                         GTGGATATTACTACGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
genomic: ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
EST: gi|5343079|gb|AI795489.1|AI795489
EST:     AGTAAAGGCACACCCTTTGAAG                         GTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
genomic: AGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
EST: gi|8103224|gb|AW927877.1|AW927877
EST:     GAAGTAAAGGCACACCCTTTGAAG                         GTGGATATTACTACGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
genomic: GAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
EST: gi|60346203|gb|DN213176.1|DN213176
EST:     ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAG                         GTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
genomic: ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
EST: gi|9742575|gb|BE518723.1|BE518723
EST:     ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAG                         GTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
genomic: ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
EST: gi|60341447|gb|DN208420.1|DN208420
EST:     ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAG                         GTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC
genomic: ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGC

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: 38 (upstream exon), 40 (downstream exon)
Score: 161

ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGCCTCCAAGTATCAG


Block sizes: 28 (upstream exon), 40 (downstream exon)
Score: 256

ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGCCTCCAAGTATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 336

ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGCCTCCAAGTATCAG


Block sizes: 28 (upstream exon), 40 (downstream exon)
Score: 175

ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatca ... ccacctgcagGTGGATATTACTATGGGAAACTCAAATTTCCACCGGATTATCCTTTTAAGCCTCCAAGTATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTATGTACTTGAAGGAAGTAAAGGCACACCCTTTGAAGgtaaagatcatatgtactataccacaatatctactccctccaatatttgtattgttacttataatctctaacaaagtttttcacgtttcaatttcccacctgcag

- - - -  TTGAAG
- - - - - - AAGGAA
- - - - - - - - - - - - - - - -  TTGAAG