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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacttaattccaaacatacatgacatcttatcagtagatgattctaacacataaccattgccttctcaccctgctttgtctttggatgctgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTTGATTGATGATACCAACACATCCAACACAATGTGTGCATGTCACATCTTT

Basic information

species Zea mays
transcript GRMZM5G858094_T02
intron # 32
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|32907858|gb|CF012671.1|CF012671
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|37391423|gb|CF632954.1|CF632954
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|31350746|gb|CD435103.1|CD435103
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|15199218|gb|BI423720.1|BI423720
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAA
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAA
EST: gi|9254948|gb|BE345416.1|BE345416
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|6012487|gb|AW061924.1|AW061924
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211003777|gb|FL418537.1|FL418537
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTTGTTCAGGAAGTCAAGAAGGTCCT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTT-GTTCAGGAAGTCAAGAAGGTCCT
EST: gi|18650380|gb|BM499199.1|BM499199
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|24764564|gb|CA399728.1|CA399728
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTTTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|32930151|gb|CF034963.1|CF034963
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAG-CGAAGTTTGTTCAGGAAGTCAAGAAGGTCCT
EST: gi|111145877|gb|EE258154.1|EE258154
EST:     TTCAGATCTGCCAGGCATTCTCGCAGGGTCTTTCTACGCTATTAGAAAAG                         ATGGAATCCCTCTCAGAGAAGCGAAGTTTGTTCAGGGAAGTCAAGGAAGGT
genomic: TTCAGATCTGCAAG-CATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGA-TCCCTCTCAGAGA-GCGAAGTTTGTTCAGG-AAGTCAAG-AAGGT
EST: gi|211035408|gb|FK972640.1|FK972640
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|5922288|gb|AW055577.1|AW055577
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTTTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|113703094|gb|EE680598.1|EE680598
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211035413|gb|FK972645.1|FK972645
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|31350902|gb|CD435259.1|CD435259
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|32940787|gb|CF045606.1|CF045606
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|24768188|gb|CA403317.1|CA403317
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211035410|gb|FK972642.1|FK972642
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|32928834|gb|CF033646.1|CF033646
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|22545794|gb|BU098168.1|BU098168
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211035420|gb|FK972652.1|FK972652
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|32945088|gb|CF049907.1|CF049907
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|31350117|gb|CD434474.1|CD434474
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211037853|gb|FK972653.1|FK972653
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|31352134|gb|CD436491.1|CD436491
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|33103482|gb|CF063442.1|CF063442
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211035414|gb|FK972646.1|FK972646
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211035418|gb|FK972650.1|FK972650
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|7138037|gb|AW499397.1|AW499397
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211153035|gb|FL370435.1|FL370435
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|4827615|gb|AI668307.1|AI668307
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|67019068|gb|CO447817.1|CO447817
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211035419|gb|FK972651.1|FK972651
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
EST: gi|211035409|gb|FK972641.1|FK972641
EST:     GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAG                         ATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT
genomic: GTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTT

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: 286

GCTTAGGGCTCAAAAAGTGTCTCATTCGCTCTCTGATCTTGCTGACTCCAGTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTTGATTGATGATACCAACACATCCAACACAATGTGTGCATGTCACATCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

GCTTAGGGCTCAAAAAGTGTCTCATTCGCTCTCTGATCTTGCTGACTCCAGTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTTGATTGATGATACCAACACATCCAACACAATGTGTGCATGTCACATCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 360

GCTTAGGGCTCAAAAAGTGTCTCATTCGCTCTCTGATCTTGCTGACTCCAGTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTTGATTGATGATACCAACACATCCAACACAATGTGTGCATGTCACATCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 378

GCTTAGGGCTCAAAAAGTGTCTCATTCGCTCTCTGATCTTGCTGACTCCAGTTCAGATCTGCAAGCATTCTCGCAGGGTCTTTCTACGCTATTAGATAAGgtaaatttgc ... tgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTTGATTGATGATACCAACACATCCAACACAATGTGTGCATGTCACATCTTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacttaattccaaacatacatgacatcttatcagtagatgattctaacacataaccattgccttctcaccctgctttgtctttggatgctgctcatcagATGGATCCCTCTCAGAGAGCGAAGTTTGTTCAGGAAGTCAAGAAGGTCCTTGATTGATGATACCAACACATCCAACACAATGTGTGCATGTCACATCTTT

- - - - - - - - atacatg
- - - - - - - - - - - - - - - - - - - -tgattct
- - - - - - - - - - - - - - - - - - - - - - - aacacat