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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgataatctgctagccagctaggaatgtcaattcgctcagcttatgtcaaatgtgttatgatttgactgctgttgatgcag

Basic information

species Zea mays
transcript GRMZM2G409104_T01
intron # 4
splice site 5'
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|78110631|gb|DV529039.1|DV529039
EST:     CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGG                         AGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
genomic: CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
EST: gi|148965278|gb|EE016081.2|EE016081
EST:     CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGG                         AGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
genomic: CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
EST: gi|89250725|gb|DY622511.1|DY622511
EST:     CTGTATACCAGCAAGGCGTGCATATCGGCTTCAAGGGACAGTACTCAGGG                         AGCAAGGAAGA-AAGCATTTCATTCACAACCACTTCACATTTC
genomic: CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTC
EST: gi|101390012|gb|EB816938.1|EB816938
EST:     CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCCGGG                         AGCAAGGAAGAGAAACATTTCATTCACAACCACTTCCCATTTCTGGTGAAG
genomic: CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
EST: gi|149013945|gb|EE043446.2|EE043446
EST:     CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGG                         AGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
genomic: CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
EST: gi|149102922|gb|EE288273.2|EE288273
EST:     CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGG                         AGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
genomic: CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
EST: gi|149096266|gb|EE181975.2|EE181975
EST:     CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGG                         AGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
genomic: CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
EST: gi|91871094|gb|EB401239.1|EB401239
EST:     CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGG                         AGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
genomic: CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
EST: gi|31353543|gb|CD437900.1|CD437900
EST:     CTGTGTACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGG                         AGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG
genomic: CTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAG

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: 34

CAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAGTATCACAAGGATGACACAGGTCTTGCCAGGATTGTTGCCTTTGAGGTTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 75

CAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAGTATCACAAGGATGACACAGGTCTTGCCAGGATTGTTGCCTTTGAGGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

CAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAGTATCACAAGGATGACACAGGTCTTGCCAGGATTGTTGCCTTTGAGGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

CAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgat ... gttgatgcagAGCAAGGAAGAGAAGCATTTCATTCACAACCACTTCACATTTCTGGTGAAGTATCACAAGGATGACACAGGTCTTGCCAGGATTGTTGCCTTTGAGGTTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCTTCCTTTGGTCGTCCCAATTAAGAGATTGGATCAAGAGGCACCTACTGTATACCAGCAAGGCGTGCATATCGGCATCAAGGGACAGTACTCAGGGgtgggtcgataatctgctagccagctaggaatgtcaattcgctcagcttatgtcaaatgtgttatgatttgactgctgttgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG