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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattacatatatgtgattaagaaatacgtacttgcatttcttgttgcccattttctgagtggtttcccctgtttagGTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAATTTGATACTAGAGATTAATGGCCTAAG

Basic information

species Zea mays
transcript GRMZM5G806257_T01
intron # 9
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|67025171|gb|CO453920.1|CO453920
EST:     CAGACAGTCTGGTTGAGGATGATGATCATATTTCTAAGTTTGAGAAAGAG                         GTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAAT
genomic: CAGACAGTCTGGTTGAGGATGATGATCATATTTCTAAGTTTGAGAAAGAGgttattacat ... ccctgtttagGTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAAT
EST: gi|32934966|gb|CF039778.1|CF039778
EST:     CAGACAGTCTGGTTGAGGATGATGATCATATTTCTAAGTTTGAGAAAGAG                         GTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAAT
genomic: CAGACAGTCTGGTTGAGGATGATGATCATATTTCTAAGTTTGAGAAAGAGgttattacat ... ccctgtttagGTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAAT
EST: gi|118406765|gb|EH038213.1|EH038213
EST:     CAGACAGCCTGGTTGGGGATGATGATCATATTTCTAAGTTTGAGAAAGAG                         GTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAAT
genomic: CAGACAGTCTGGTTGAGGATGATGATCATATTTCTAAGTTTGAGAAAGAGgttattacat ... ccctgtttagGTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAAT

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), 48 (downstream exon)
Score: 134

GTCAGAAGATGAATCCAACAATCCAACTCTACCAGATAAAGATGATTCTTCAGACAGTCTGGTTGAGGATGATGATCATATTTCTAAGTTTGAGAAAGAGgttattacat ... ccctgtttagGTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAATTTGATACTAGAGATTAATGGCCTAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 93

GTCAGAAGATGAATCCAACAATCCAACTCTACCAGATAAAGATGATTCTTCAGACAGTCTGGTTGAGGATGATGATCATATTTCTAAGTTTGAGAAAGAGgttattacat ... ccctgtttagGTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAATTTGATACTAGAGATTAATGGCCTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 148

GTCAGAAGATGAATCCAACAATCCAACTCTACCAGATAAAGATGATTCTTCAGACAGTCTGGTTGAGGATGATGATCATATTTCTAAGTTTGAGAAAGAGgttattacat ... ccctgtttagGTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAATTTGATACTAGAGATTAATGGCCTAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 85

GTCAGAAGATGAATCCAACAATCCAACTCTACCAGATAAAGATGATTCTTCAGACAGTCTGGTTGAGGATGATGATCATATTTCTAAGTTTGAGAAAGAGgttattacat ... ccctgtttagGTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAATTTGATACTAGAGATTAATGGCCTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatacgtacttgcatttcttgttgcccattttctgagtggtttcccctgtttagGTGGAAGAGACATTCCAACGAGCTCTGGGTGGCGGCGTTAATCGAGATAATTTGATACTAGAGATTAATGGCCTAAG
                                         tttcccctgttt  CT-rich tract
              atttctt  TA-rich tract