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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcatgtattatcagatgcattgatacaatatgatgatctgcactagcattcaacttctgaattttcacatctaatatcgagtttttggtgttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGCTGATGAATGGGATATGTTGTCCCTGACTTCATCAATATATGCTAGCCCA

Basic information

species Zea mays
transcript GRMZM2G320949_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|211242158|gb|FL238831.1|FL238831
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAA
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAA
EST: gi|211239922|gb|FL238817.1|FL238817
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211239921|gb|FL238816.1|FL238816
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|37416788|gb|CF646045.1|CF646045
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211239920|gb|FL238815.1|FL238815
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|89250746|gb|DY622532.1|DY622532
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|50330526|gb|CO525652.1|CO525652
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211239912|gb|FL238807.1|FL238807
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242149|gb|FL238822.1|FL238822
EST:     CGATCGACCCGGCCTCG-CSGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211239914|gb|FL238809.1|FL238809
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242152|gb|FL238825.1|FL238825
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211239917|gb|FL238812.1|FL238812
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242148|gb|FL238821.1|FL238821
EST:     CGATCGACCCGGCCTCGSSGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|94478469|gb|EB707427.1|EB707427
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211244382|gb|FL238833.1|FL238833
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242156|gb|FL238829.1|FL238829
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211244383|gb|FL238834.1|FL238834
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242150|gb|FL238823.1|FL238823
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|19770153|gb|BQ034874.1|BQ034874
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTG-GCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242153|gb|FL238826.1|FL238826
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242145|gb|FL238818.1|FL238818
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211244384|gb|FL238835.1|FL238835
EST:     CGATCGACCCGGCCTCG--SGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242147|gb|FL238820.1|FL238820
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|19822363|gb|BQ048387.1|BQ048387
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211239918|gb|FL238813.1|FL238813
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242151|gb|FL238824.1|FL238824
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211239913|gb|FL238808.1|FL238808
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242155|gb|FL238828.1|FL238828
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|13237173|gb|BG355187.1|BG355187
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242146|gb|FL238819.1|FL238819
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211242159|gb|FL238832.1|FL238832
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
EST: gi|211239915|gb|FL238810.1|FL238810
EST:     CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAG                         GTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC
genomic: CGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGC

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: 51

GCCAAATTGCCCCCGACTCAAGCCCCCCGCGCCGCCGGCGTTGGTGGAATCGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGCTGATGAATGGGATATGTTGTCCCTGACTTCATCAATATATGCTAGCCCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 87

GCCAAATTGCCCCCGACTCAAGCCCCCCGCGCCGCCGGCGTTGGTGGAATCGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGCTGATGAATGGGATATGTTGTCCCTGACTTCATCAATATATGCTAGCCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

GCCAAATTGCCCCCGACTCAAGCCCCCCGCGCCGCCGGCGTTGGTGGAATCGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGCTGATGAATGGGATATGTTGTCCCTGACTTCATCAATATATGCTAGCCCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 63

GCCAAATTGCCCCCGACTCAAGCCCCCCGCGCCGCCGGCGTTGGTGGAATCGATCGACCCGGCCTCGCCGGACAATCCACCAGCGTTGGTTTCACCTCAGgtaccgacct ... gttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGCTGATGAATGGGATATGTTGTCCCTGACTTCATCAATATATGCTAGCCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcattcaacttctgaattttcacatctaatatcgagtttttggtgttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGCTGATGAATGGGATATGTTGTCCCTGACTTCATCAATATATGCTAGCCCA
                        atctaat  putative branch site (score: 63)
                        atctaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcatgtattatcagatgcattgatacaatatgatgatctgcactagcattcaacttctgaattttcacatctaatatcgagtttttggtgttttggtagGTTTTTGTGCATGGAAGATGACAATGAGGTCACTGGAGAGTCACCTGTGGCTGATGAATGGGATATGTTGTCCCTGACTTCATCAATATATGCTAGCCCA

-gcatgta
- - - - - - cagatgc
- - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - ctgcact
- - - - - - - - - - - - - - - - - - - - - - - gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - cttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttttg