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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatattggatgcatcgacccttcaacattgatacgttgctgaagaatattttttttcatcctttcattgcaaatgtgaatttattgaagctacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCT

Basic information

species Zea mays
transcript GRMZM5G823750_T02
intron # 4
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|211540347|gb|FL091515.1|FL091515
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211540346|gb|FL091514.1|FL091514
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|78116158|gb|DV534546.1|DV534546
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|78120227|gb|DV538611.1|DV538611
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211540349|gb|FL091517.1|FL091517
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAAGCCTGTGCTAATGAAACCTGGCATNCA-
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCAT-CAA
EST: gi|76013572|gb|DT940742.1|DT940742
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|29576943|gb|CB617055.1|CB617055
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543360|gb|FL091529.1|FL091529
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAA
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAA
EST: gi|6022643|gb|AW067455.1|AW067455
EST:     GGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGGTTATG                         GCTACGGTTTTATTGGCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: GGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543361|gb|FL091530.1|FL091530
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|101385030|gb|EB814560.1|EB814560
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|84980380|gb|DW530729.1|DW530729
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTATTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543355|gb|FL091524.1|FL091524
EST:     ATTGCTTGGGCGTCCAACTAATTCTCTATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543350|gb|FL091519.1|FL091519
EST:     ATTGCTTGGGCGTCCAACTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543352|gb|FL091521.1|FL091521
EST:     ATTGCTTGGGCGTCCAACTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211540348|gb|FL091516.1|FL091516
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543357|gb|FL091526.1|FL091526
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGT
EST: gi|211543362|gb|FL091531.1|FL091531
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|6056596|gb|AW091001.1|AW091001
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543353|gb|FL091522.1|FL091522
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGC-TGTGCTAATGAAAC-TGGCATC
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATC
EST: gi|211543349|gb|FL091518.1|FL091518
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGC
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGC
EST: gi|76011928|gb|DT939098.1|DT939098
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGTCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|60351828|gb|DN218801.1|DN218801
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|91050221|gb|EB160639.1|EB160639
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|78116574|gb|DV534961.1|DV534961
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTCGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543359|gb|FL091528.1|FL091528
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543351|gb|FL091520.1|FL091520
EST:     ATTGCTTGGGCGTCCAACTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
EST: gi|211543354|gb|FL091523.1|FL091523
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAA
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAA
EST: gi|33770746|gb|CF273040.1|CF273040
EST:     ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG                         GCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT
genomic: ATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAAT

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: 47 (upstream exon), 49 (downstream exon)
Score: 68

GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 69

GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCT


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

GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 54

GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATGgtaaatctca ... tacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattttttttcatcctttcattgcaaatgtgaatttattgaagctacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCT
                                            ctacttctc  CT-rich tract
                         aaatgtgaatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatattggatgcatcgacccttcaacattgatacgttgctgaagaatattttttttcatcctttcattgcaaatgtgaatttattgaagctacttctcagGCTACGGTTTTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT