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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatatttaaacaccatatagtgtttttgtgacgggtgtatgcatgagtgtcccttatattgggttttgctgtatgttgtgtctttgccatgcatcct...

Basic information

species Zea mays
transcript GRMZM2G358059_T01
intron # 11
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|148931875|gb|EC877339.2|EC877339
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|84980101|gb|DW530450.1|DW530450
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|86467986|gb|DY234356.1|DY234356
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|149074502|gb|EE162898.2|EE162898
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|14190892|gb|BG833122.1|BG833122
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGCAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGCTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCG-AGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGG-TGGGGATGATGAGGATGATGACCTAGAG
EST: gi|7162446|gb|AW520068.1|AW520068
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|14190894|gb|BG833124.1|BG833124
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|37377946|gb|CF625620.1|CF625620
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|33096251|gb|CF056245.1|CF056245
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|149074540|gb|EE162939.2|EE162939
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|86470502|gb|DY236872.1|DY236872
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|71442155|gb|DR823205.1|DR823205
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|37374548|gb|CF623645.1|CF623645
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|14190893|gb|BG833123.1|BG833123
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|84980095|gb|DW530444.1|DW530444
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|84976665|gb|DW475087.1|DW475087
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATG
EST: gi|15590491|gb|BI675107.1|BI675107
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|5268655|gb|AI770619.1|AI770619
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|33093443|gb|CF053437.1|CF053437
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|148937046|gb|EC881219.2|EC881219
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|21088786|gb|BQ401099.1|BQ401099
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATG
EST: gi|211100469|gb|FL191950.1|FL191950
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|84980708|gb|DW531057.1|DW531057
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|29544799|gb|CB605407.1|CB605407
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|37382092|gb|CF627969.1|CF627969
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|88750940|gb|DY535081.1|DY535081
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|71759740|gb|DR957677.1|DR957677
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAA-GGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|7162466|gb|AW520088.1|AW520088
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAGAAGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|148963936|gb|EE015057.2|EE015057
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
EST: gi|71432522|gb|DR813572.1|DR813572
EST:     GCAGAAAAGGCTGCTTTTGATGAGGCCGAGNNNNNNNNNGGAAGAAGAG                         GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG
genomic: GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAA-GGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG

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: 1877

GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1337

GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1244

GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 5985

GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatattt ... ttgtcaacagGATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAAAAGGCTGCTTTTGATGAGGCCGAGAAAAAAAAGGAAGAAGAGgtatatatttaaacaccatatagtgtttttgtgacgggtgtatgcatgagtgtcccttatattgggttttgctgtatgttgtgtctttgccatgcatcct

- - - -  GCTGCT
- - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - AAGAAG