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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTGCCTTGCCCACCTTCTCATACTGCCGTAGGAGGTCCAGCTTCACTCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttttattcacagaagctgaatataagtgcaaatgctttgtttgttcttagcatttggtttattgaattaattcattttgttggatttcaatcc...

Basic information

species Zea mays
transcript GRMZM2G070378_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|211362406|gb|FL344697.1|FL344697
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211155533|gb|FL327677.1|FL327677
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211475243|gb|FL335043.1|FL335043
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|18167419|gb|BM337258.1|BM337258
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211049868|gb|FL342249.1|FL342249
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211090846|gb|FL316187.1|FL316187
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211155695|gb|FL336009.1|FL336009
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCAC
EST: gi|211211167|gb|FL351365.1|FL351365
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|18166077|gb|BM335916.1|BM335916
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211096078|gb|FL328998.1|FL328998
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGASGCTATTATG                         CTGGGGGGCTCCATCTGATATCWCCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211033675|gb|FL344500.1|FL344500
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211129076|gb|FL366496.1|FL366496
EST:     TCCYTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211251061|gb|FL352807.1|FL352807
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211230922|gb|FL338414.1|FL338414
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211275935|gb|FL328144.1|FL328144
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211399575|gb|FL345591.1|FL345591
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211049600|gb|FL335096.1|FL335096
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|32863181|gb|CF002863.1|CF002863
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATTTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
EST: gi|211111367|gb|FL325871.1|FL325871
EST:     TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC
genomic: TCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAAC

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: 107

TGATGTGCCTTGCCCACCTTCTCATACTGCCGTAGGAGGTCCAGCTTCACTCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAACATCAATAAGATTGTATGCCTGAGCTTATTGCCTTTGACCTCTGAAAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 174

TGATGTGCCTTGCCCACCTTCTCATACTGCCGTAGGAGGTCCAGCTTCACTCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAACATCAATAAGATTGTATGCCTGAGCTTATTGCCTTTGACCTCTGAAAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 114

TGATGTGCCTTGCCCACCTTCTCATACTGCCGTAGGAGGTCCAGCTTCACTCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAACATCAATAAGATTGTATGCCTGAGCTTATTGCCTTTGACCTCTGAAAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 135

TGATGTGCCTTGCCCACCTTCTCATACTGCCGTAGGAGGTCCAGCTTCACTCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgccttgcagCTGGGGGGCTCCATCTGATATCACCTCATATGAATTGGAAATTCTAGGAACATCAATAAGATTGTATGCCTGAGCTTATTGCCTTTGACCTCTGAAAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGTGCCTTGCCCACCTTCTCATACTGCCGTAGGAGGTCCAGCTTCACTCCTTCCTAAGCGCAAACCCCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttttattcacagaagctgaatataagtgcaaatgctttgtttgttcttagcatttggtttattgaattaattcattttgttggatttcaatcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA