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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCAGGACGTATACAAAATCAGAGTGGATAACTACAAGCCATTCGAGCATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgatacactatcctgttgccacttctctatgttttggcgagttctaacggaatggaggagctataaactcattgatcgatgtgtaagacatggaa...

Basic information

species Zea mays
transcript GRMZM2G000749_T02
intron # 1
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|211270555|gb|FL015563.1|FL015563
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211268121|gb|FL015554.1|FL015554
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211265687|gb|FL015541.1|FL015541
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211270558|gb|FL015566.1|FL015566
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211265690|gb|FL015544.1|FL015544
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211268118|gb|FL015551.1|FL015551
EST:     ATGTCTGGCTGGAGCGCAGCGAANACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211265688|gb|FL015542.1|FL015542
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211270568|gb|FL015576.1|FL015576
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|60338799|gb|DN205772.1|DN205772
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211270566|gb|FL015574.1|FL015574
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211270559|gb|FL015567.1|FL015567
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211268127|gb|FL015560.1|FL015560
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211265692|gb|FL015546.1|FL015546
EST:     ATGTCTGGCTGGAGCGCAGCGAANACGGCACCCGACGTGTTCNCCCGCTG                         GAAAACCTGCCTGGTTGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTG-TTGAA
EST: gi|211270561|gb|FL015569.1|FL015569
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211265693|gb|FL015547.1|FL015547
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211270567|gb|FL015575.1|FL015575
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211270560|gb|FL015568.1|FL015568
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211265691|gb|FL015545.1|FL015545
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
EST: gi|211270564|gb|FL015572.1|FL015572
EST:     ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTG                         GAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA
genomic: ATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAA

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: 46 (upstream exon), 49 (downstream exon)
Score: 72

GCCGCAGGACGTATACAAAATCAGAGTGGATAACTACAAGCCATTCGAGCATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAACCAGTGAAGCCAGCTGATTTAGAGGATACACCATTTACGCTGGTTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 100

GCCGCAGGACGTATACAAAATCAGAGTGGATAACTACAAGCCATTCGAGCATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAACCAGTGAAGCCAGCTGATTTAGAGGATACACCATTTACGCTGGTTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

GCCGCAGGACGTATACAAAATCAGAGTGGATAACTACAAGCCATTCGAGCATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAACCAGTGAAGCCAGCTGATTTAGAGGATACACCATTTACGCTGGTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GCCGCAGGACGTATACAAAATCAGAGTGGATAACTACAAGCCATTCGAGCATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgata ... tttgttgcagGAAAACCTGCCTGTTGAACAGTTCGTTGACAGAAATGTTCCTGACAGAGAACCAGTGAAGCCAGCTGATTTAGAGGATACACCATTTACGCTGGTTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCAGGACGTATACAAAATCAGAGTGGATAACTACAAGCCATTCGAGCATGTCTGGCTGGAGCGCAGCGAAGACGGCACCCGACGTGTTCACCCGCTGgtcagtgatacactatcctgttgccacttctctatgttttggcgagttctaacggaatggaggagctataaactcattgatcgatgtgtaagacatggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA