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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattgcatatatctagcatgtctttctgatattctgaatctcattttagcccttgtgattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCGATCCATAAATTAGAG

Basic information

species Zea mays
transcript GRMZM2G003734_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003734_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g14654.2 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------------------------------------------------------gtactattgcatatatctagcatgt-ctttctgatattctgaatctcattttagcccttgtgattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCGATCCATAAATTAGAG
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gtactaatccatactagtgcatattccctccgtcccaaaatataagcattttttgctatgaatctagagaactatgtgtccagattcatagctaaaagttgttatattttgggacggaggtagtatattcataatattgatataaatcttactggagc----atgatttt-cagGAATGCCTTATTGAAGGGGATACTAGTTCTGTTTGGCATGTTGCAAAAGCTATCCATAAGTTAGAG
















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|148972311|gb|EE023217.2|EE023217
EST:     TTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAG                         GAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCG
genomic: TTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAGgtactattgc ... gattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCG
EST: gi|4646871|gb|AI621946.1|AI621946
EST:     CTTGAACTTGA-CATTTTTTGCAG                         GAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCG
genomic: CTTGAACTTGACCATTCTTTGCAGgtactattgc ... gattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCG
EST: gi|32932185|gb|CF036997.1|CF036997
EST:     TTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAG                         GAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCG
genomic: TTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAGgtactattgc ... gattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCG
EST: gi|33091408|gb|CF051402.1|CF051402
EST:     TTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAG                         GAATGCCTTATTGAAGGAGATACAAGTTCTGTCTGGCATGTTGCTAAAGCG
genomic: TTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAGgtactattgc ... gattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCG

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: 114

AGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCCTTATATCTAGTTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAGgtactattgc ... gattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCGATCCATAAATTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

AGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCCTTATATCTAGTTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAGgtactattgc ... gattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCGATCCATAAATTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

AGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCCTTATATCTAGTTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAGgtactattgc ... gattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCGATCCATAAATTAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 116

AGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCCTTATATCTAGTTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACCATTCTTTGCAGgtactattgc ... gattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCGATCCATAAATTAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctagcatgtctttctgatattctgaatctcattttagcccttgtgattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCGATCCATAAATTAGAG
            ttctgat  putative branch site (score: 116)
                                            tgattttata  TA-rich tract