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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttggagctttcccagttcgtggattaacgctgtgggtaccttgcattgcagaaaaagaggcaactctgggggaataacggatttcaccttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCACAAAGCATATGTTGTGATTTGTCGATGGCGAGGAGATGAAACAGGTGTA

Basic information

species Zea mays
transcript GRMZM2G138505_T01
intron # 1
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|211238206|gb|FL261937.1|FL261937
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211235958|gb|FL261916.1|FL261916
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|9254424|gb|BE344892.1|BE344892
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGTAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211238196|gb|FL261927.1|FL261927
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAAATTGGAGGTTGTCACCATCACC
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAA-TTGGAGGTTGTCACCATCACC
EST: gi|211235956|gb|FL261914.1|FL261914
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211238199|gb|FL261930.1|FL261930
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211240433|gb|FL261940.1|FL261940
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|88751194|gb|DY535335.1|DY535335
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCGGGGCCTGG                         GTTACTGCGTGACATGTAATATTGTATAATTGGAGGTTGTCCCCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|149081143|gb|EE170252.2|EE170252
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211235960|gb|FL261918.1|FL261918
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211235957|gb|FL261915.1|FL261915
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|101387923|gb|EB815975.1|EB815975
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211235965|gb|FL261923.1|FL261923
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211235967|gb|FL261925.1|FL261925
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|78081340|gb|DV509752.1|DV509752
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211235963|gb|FL261921.1|FL261921
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211238200|gb|FL261931.1|FL261931
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGGTATAATTGGAGGTTGTCACCATCACC
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATT-GTATAATTGGAGGTTGTCACCATCACC
EST: gi|71772237|gb|DR970174.1|DR970174
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211240434|gb|FL261941.1|FL261941
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211238207|gb|FL261938.1|FL261938
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211235964|gb|FL261922.1|FL261922
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211238202|gb|FL261933.1|FL261933
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|31355242|gb|CD439599.1|CD439599
EST:     GCGCCCCGCCGGATTCACCTCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|211238208|gb|FL261939.1|FL261939
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
EST: gi|71447439|gb|DR828489.1|DR828489
EST:     GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGG                         GTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA
genomic: GCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCA

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: 119

ATCTCGCCGGCGACAGACACCAGATCTCGCCGCCCGTTGCGCGCCGATACGCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCACAAAGCATATGTTGTGATTTGTCGATGGCGAGGAGATGAAACAGGTGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

ATCTCGCCGGCGACAGACACCAGATCTCGCCGCCCGTTGCGCGCCGATACGCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCACAAAGCATATGTTGTGATTTGTCGATGGCGAGGAGATGAAACAGGTGTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55

ATCTCGCCGGCGACAGACACCAGATCTCGCCGCCCGTTGCGCGCCGATACGCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCACAAAGCATATGTTGTGATTTGTCGATGGCGAGGAGATGAAACAGGTGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

ATCTCGCCGGCGACAGACACCAGATCTCGCCGCCCGTTGCGCGCCGATACGCGCCCCGCCGGATTCACCGCTCCTCGCGCTGCAGCACGCCCGGGCCTGGgtaagtttat ... ttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCACAAAGCATATGTTGTGATTTGTCGATGGCGAGGAGATGAAACAGGTGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgcagaaaaagaggcaactctgggggaataacggatttcaccttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCACAAAGCATATGTTGTGATTTGTCGATGGCGAGGAGATGAAACAGGTGTA
                            gaataac  putative branch site (score: 120)
                                      tttcacctt  putative PPT
      agaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttggagctttcccagttcgtggattaacgctgtgggtaccttgcattgcagaaaaagaggcaactctgggggaataacggatttcaccttgtttacagGTTACTGCGTGACATGTAGTATTGTATAATTGGAGGTTGTCACCATCACCACAAAGCATATGTTGTGATTTGTCGATGGCGAGGAGATGAAACAGGTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- -tggagct
- - - - - - - - - - - - - - -cgctgtg
- - - - - - - - - - - - - - - - - - - - - ttgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa