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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcatactcacttcaagttttcttgagtgttcttctggtcatggaagtaaaatctggtatgcttaccgttgatgcgtatcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCTTGATTGACTTACTAGATCTCCGCAAACTGCTCGGTCAGAAGAGGAAAGC

Basic information

species Zea mays
transcript GRMZM2G026311_T02
intron # 3
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|50326903|gb|CO522029.1|CO522029
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|71297620|gb|DR784761.1|DR784761
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|87155520|gb|DY400309.1|DY400309
EST:     GGAGTCTGGGCAGAAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGGTACCAGATCACATAATGGTGGCT
genomic: GGAGTCTGGGCAG-AACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|78081791|gb|DV510203.1|DV510203
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|78088648|gb|DV517041.1|DV517041
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|148962831|gb|EE013751.2|EE013751
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|78123039|gb|DV541423.1|DV541423
EST:     GGAGTCTGGGCAGAACTTCTAGGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAGTGGTGGCT
genomic: GGAGTCTGGGCAGAACTTCTAGGG-ATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|78087906|gb|DV516299.1|DV516299
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|71306682|gb|DR789502.1|DR789502
EST:     AGGAGTCTGGGCAAAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGATGACATATGCATTGGTACC
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACC
EST: gi|5018429|gb|AI714622.1|AI714622
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGGTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|71330916|gb|DR802256.1|DR802256
EST:     GGATTGGTG-CTTTTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: GGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|71330918|gb|DR802257.1|DR802257
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|76021477|gb|DT948647.1|DT948647
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|101399591|gb|EB821646.1|EB821646
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|76013036|gb|DT940206.1|DT940206
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|93011965|gb|EB637485.1|EB637485
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|50336717|gb|CO531843.1|CO531843
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT
EST: gi|78026633|gb|DV495020.1|DV495020
EST:     AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTG                         GGGTTCAGATAGTTGACATATGCATTGGTACCAGATCACATAATGGTGGCT
genomic: AGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCT

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), 44 (downstream exon)
Score: 46

TTCCATGAGATGTGCGCAAAAGTCGGAGTAGATCCATTGGCATCTAATAAAGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCTTGATTGACTTACTAGATCTCCGCAAACTGCTCGGTCAGAAGAGGAAAGC


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

TTCCATGAGATGTGCGCAAAAGTCGGAGTAGATCCATTGGCATCTAATAAAGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCTTGATTGACTTACTAGATCTCCGCAAACTGCTCGGTCAGAAGAGGAAAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

TTCCATGAGATGTGCGCAAAAGTCGGAGTAGATCCATTGGCATCTAATAAAGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCTTGATTGACTTACTAGATCTCCGCAAACTGCTCGGTCAGAAGAGGAAAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

TTCCATGAGATGTGCGCAAAAGTCGGAGTAGATCCATTGGCATCTAATAAAGGAGTCTGGGCAGAACTTCTAGGGATTGGTGACTTCTACTATGAACTTGgttggcatac ... atcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCTTGATTGACTTACTAGATCTCCGCAAACTGCTCGGTCAGAAGAGGAAAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctggtcatggaagtaaaatctggtatgcttaccgttgatgcgtatcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCTTGATTGACTTACTAGATCTCCGCAAACTGCTCGGTCAGAAGAGGAAAGC
            aagtaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggcatactcacttcaagttttcttgagtgttcttctggtcatggaagtaaaatctggtatgcttaccgttgatgcgtatcgtggcagGGGTTCAGATAGTTGACATATGCATTGCTACCAGATCACATAATGGTGGCTTGATTGACTTACTAGATCTCCGCAAACTGCTCGGTCAGAAGAGGAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA