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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgcgcttctgatttgtgctgtttctcggaaaggggtgggctttgggcatctttgtgatagctctggcttacttttatgttttggcaatgcagGGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATGGATATTGATAGTGCAGACTCGGGGAACCCGCTTGCAGCAACAGAATATG

Basic information

species Zea mays
transcript GRMZM2G061287_T01
intron # 5
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|61118385|gb|DN559346.1|DN559346
EST:     ACGTGGAACTGGGCGAGCCGGTCGACGATAGTGATAGTGACATCGACATG                         GGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATG
genomic: ACGTGGAACTGGACGAGCCGGTCGACGATAGTGATTGTGACGTCGACATGgtaattgcgc ... ggcaatgcagGGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATG
EST: gi|60394849|gb|DN227718.1|DN227718
EST:     GATAGTGATTGTGACGTCGACATG                         GGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATG
genomic: GATAGTGATTGTGACGTCGACATGgtaattgcgc ... ggcaatgcagGGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATG
EST: gi|78119998|gb|DV538382.1|DV538382
EST:     ACGTGGAACTGGACGAGCCGGTCGACGATAGTGATTGTGACGTCGACATG                         GGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATG
genomic: ACGTGGAACTGGACGAGCCGGTCGACGATAGTGATTGTGACGTCGACATGgtaattgcgc ... ggcaatgcagGGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATG

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: 48 (upstream exon), 49 (downstream exon)
Score: 87

CGGAGTTGATCAACGGAAGGAACCAATCGGCGATGGCATCATTGATATCGACGTGGAACTGGACGAGCCGGTCGACGATAGTGATTGTGACGTCGACATGgtaattgcgc ... ggcaatgcagGGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATGGATATTGATAGTGCAGACTCGGGGAACCCGCTTGCAGCAACAGAATATG


Block sizes: 37 (upstream exon), 48 (downstream exon)
Score: 10

CGGAGTTGATCAACGGAAGGAACCAATCGGCGATGGCATCATTGATATCGACGTGGAACTGGACGAGCCGGTCGACGATAGTGATTGTGACGTCGACATGgtaattgcgc ... ggcaatgcagGGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATGGATATTGATAGTGCAGACTCGGGGAACCCGCTTGCAGCAACAGAATATG


Block sizes: 30 (upstream exon), 41 (downstream exon)
Score: 6

CGGAGTTGATCAACGGAAGGAACCAATCGGCGATGGCATCATTGATATCGACGTGGAACTGGACGAGCCGGTCGACGATAGTGATTGTGACGTCGACATGgtaattgcgc ... ggcaatgcagGGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATGGATATTGATAGTGCAGACTCGGGGAACCCGCTTGCAGCAACAGAATATG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 10

CGGAGTTGATCAACGGAAGGAACCAATCGGCGATGGCATCATTGATATCGACGTGGAACTGGACGAGCCGGTCGACGATAGTGATTGTGACGTCGACATGgtaattgcgc ... ggcaatgcagGGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATGGATATTGATAGTGCAGACTCGGGGAACCCGCTTGCAGCAACAGAATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctttgggcatctttgtgatagctctggcttacttttatgttttggcaatgcagGGTGATGAGACAGAGAACAAGGACATTATGAACCAAGATGAATCGCTCATGGATATTGATAGTGCAGACTCGGGGAACCCGCTTGCAGCAACAGAATATG
                           ggcttac  putative branch site (score: 10)
 ttacttttatgtttt  TA-rich tract