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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggaactagtgcttataattgtgtcttactgcctcataatttggtgttgttttgttaatcagtactgtttctaattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAGGTCTTGGTCTTCTCGGCCATTGCCATGGGATTGGTGTTTGTCGGTTCTT

Basic information

species Zea mays
transcript GRMZM2G155384_T01
intron # 16
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|32940220|gb|CF045039.1|CF045039
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
EST: gi|32943723|gb|CF048542.1|CF048542
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
EST: gi|32929231|gb|CF034043.1|CF034043
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
EST: gi|32848175|gb|CD987856.1|CD987856
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
EST: gi|32928692|gb|CF033504.1|CF033504
EST:     GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAG                         CTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG
genomic: GAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAG

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: 993

TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAGGTCTTGGTCTTCTCGGCCATTGCCATGGGATTGGTGTTTGTCGGTTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 828

TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAGGTCTTGGTCTTCTCGGCCATTGCCATGGGATTGGTGTTTGTCGGTTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 467

TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAGGTCTTGGTCTTCTCGGCCATTGCCATGGGATTGGTGTTTGTCGGTTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 748

TGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAGAAGAGgtgggaacta ... taattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAGGTCTTGGTCTTCTCGGCCATTGCCATGGGATTGGTGTTTGTCGGTTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgcctcataatttggtgttgttttgttaatcagtactgtttctaattttcagCTTAAAATGCATCTATCTGCTGTGTTGGGAGACTCCCAATCACCTCTTGAGGTCTTGGTCTTCTCGGCCATTGCCATGGGATTGGTGTTTGTCGGTTCTT
                                          ttctaat  putative branch site (score: 748)
                                      ctgtttct  CT-rich tract
                                         tttctaatttt  TA-rich tract