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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaacacagcgagctccggttctaacatctggttgctcagcagttaaaacttaaagtttggtaccccagtccccttttctcatcattatcttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG

Basic information

species Zea mays
transcript GRMZM2G003692_T07
intron # 9
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|12968787|gb|BG265824.1|BG265824
EST:     GCTGCAGCTTTTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACCATT
genomic: GCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|37376662|gb|CF624883.1|CF624883
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|14244326|gb|BG842296.2|BG842296
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|5343223|gb|AI795408.1|AI795408
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|14208321|gb|BG842006.1|BG842006
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|113703640|gb|EE681144.1|EE681144
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|32940746|gb|CF045565.1|CF045565
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|88757473|gb|DY541614.1|DY541614
EST:     CACTACAATCTTCTGTTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|37397592|gb|CF636096.1|CF636096
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|32909212|gb|CF014024.1|CF014024
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|32856130|gb|CD995811.1|CD995811
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|88757474|gb|DY541615.1|DY541615
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|6101980|gb|AW126450.1|AW126450
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|88753506|gb|DY537647.1|DY537647
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|40337101|gb|CK371171.1|CK371171
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|37390564|gb|CF632514.1|CF632514
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|67023347|gb|CO452096.1|CO452096
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|31362808|gb|CD447165.1|CD447165
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAGCGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|6022668|gb|AW067596.1|AW067596
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|32864069|gb|CF003751.1|CF003751
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|71759817|gb|DR957754.1|DR957754
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|211078663|gb|FL128724.1|FL128724
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|78021266|gb|DV489653.1|DV489653
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|211495955|gb|FL480154.1|FL480154
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATTGCAAACACATTTTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|6095476|gb|AW120143.1|AW120143
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|6194694|gb|AW146798.1|AW146798
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|5915523|gb|AW053164.1|AW053164
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|211078661|gb|FL128722.1|FL128722
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         CAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|93015973|gb|EB641493.1|EB641493
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACCCATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|37387558|gb|CF630976.1|CF630976
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAG                         -A-AA-CGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
EST: gi|60353742|gb|DN220715.1|DN220715
EST:     CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCT--G                         -AGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT
genomic: CACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATT

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: 48 (upstream exon), 47 (downstream exon)
Score: 39

GTGTACAAAAGGCATTAAGGTCACTGTTATCTGCCCTGGACCGATTGAAACACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 120

GTGTACAAAAGGCATTAAGGTCACTGTTATCTGCCCTGGACCGATTGAAACACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 146

GTGTACAAAAGGCATTAAGGTCACTGTTATCTGCCCTGGACCGATTGAAACACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 132

GTGTACAAAAGGCATTAAGGTCACTGTTATCTGCCCTGGACCGATTGAAACACTACAATCTTCTGCTGCAGCTTCTTCATCGCAAACACATTCTGCTGAGgttatccctg ... ttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacttaaagtttggtaccccagtccccttttctcatcattatcttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG
                        tccccttttctcatca  CT-rich tract
     ttaaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaacacagcgagctccggttctaacatctggttgctcagcagttaaaacttaaagtttggtaccccagtccccttttctcatcattatcttcctcacagCAGAAACGTGAGAAACGTGTTTCGGTGGAACGGTGTGTTGAACTGACAATTGTTGCTGCTACTCATGGACTGAAAGAAGCATGGATATCATATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
-caacaca
- - - - - - gctccgg
- - - - - - - - - - - - - - -tggttgc
- - - - - - - - - - - - - - - - - - tcagcag