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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgactgtattgttatgatctttattttagaggaattttgatactatgatgaacataaatcttttacggcttattttgtttcatgttttaacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG

Basic information

species Zea mays
transcript GRMZM2G036206_T01
intron # 19
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|78180678|gb|DV551006.1|DV551006
EST:     GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT                         AATTGCGGGATACCATTGT
genomic: GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagA-TTGCGGGATACCATTGT
EST: gi|7844204|gb|AW787426.1|AW787426
EST:     GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT                         ATTGCGGGATACCATTGTTCTAGTACTAAGGCTGTTCAAAAATATG
genomic: GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
EST: gi|211089151|gb|FL459717.1|FL459717
EST:     GCATCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT                         ATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
genomic: GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
EST: gi|113602419|gb|DW767581.1|DW767581
EST:     GTTATAATCTGAAGCCAGTAGAAAATACACT                         ATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
genomic: GTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
EST: gi|5762226|gb|AI967274.1|AI967274
EST:     GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT                         ATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
genomic: GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
EST: gi|71772016|gb|DR969953.1|DR969953
EST:     GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT                         ATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
genomic: GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
EST: gi|5871151|gb|AW017592.1|AW017592
EST:     GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT                         ATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
genomic: GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
EST: gi|6020497|gb|AW065425.1|AW065425
EST:     GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT                         ATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
genomic: GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
EST: gi|7844205|gb|AW787427.1|AW787427
EST:     GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACT                         ATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
genomic: GCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG

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), 48 (downstream exon)
Score: 38

ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 67

ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG


Block sizes: 35 (upstream exon), 48 (downstream exon)
Score: 24

ATTCATATTCCATATGGGCGTCCAACAGAGTTCTCGATTACATCTGCTGCGTCTGCTGATGGTGTCAGTTATAATCTGAAGCCAGTAGAAAATACACTgtgagtatca ... aacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatgaacataaatcttttacggcttattttgtttcatgttttaacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG
                                         ttttaac  putative branch site (score: 24)
                                               cttttc  CT-rich tract
                          ttattttgtttcatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgactgtattgttatgatctttattttagaggaattttgatactatgatgaacataaatcttttacggcttattttgtttcatgttttaacttttcagATTGCGGGATACCATTGTTCTAGTACTAAGGTTGTTCAAAAATATG

- - - tgtattg
- - - - - - - - - - - - - - - - - - - -tgatact
- - - - - - - - - - - - - - - - - - - - - - - -tgatgaa