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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgtgtttctttgacctagaaccatgaagagaactcattacaccatgaatccttatggagcttctaaaatgtgcttccatccacag

Basic information

species Zea mays
transcript GRMZM2G137707_T01
intron # 9
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|4646576|gb|AI491372.2|AI491372
EST:     TTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: TTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|67012698|gb|CO441447.1|CO441447
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGGTTGCCGAG                         -TTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGG-TTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|149107024|gb|EE188919.2|EE188919
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|71774748|gb|DR972626.1|DR972626
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|89106092|gb|DY576309.1|DY576309
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|88747666|gb|DY531807.1|DY531807
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|78108108|gb|DV526526.1|DV526526
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|17931045|gb|BM268005.1|BM268005
EST:     TCCCACAGCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: TCCCACAGCTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|32936074|gb|CF040886.1|CF040886
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|71442203|gb|DR823253.1|DR823253
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|33093800|gb|CF053794.1|CF053794
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGT
EST: gi|14204187|gb|BG837864.1|BG837864
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|32937138|gb|CF041957.1|CF041957
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|91874804|gb|EB404761.1|EB404761
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATTTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|18172389|gb|BM347777.1|BM347777
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|78122709|gb|DV541093.1|DV541093
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|67041530|gb|CO467785.1|CO467785
EST:     CCAAGACATTGGCCGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTCGG
genomic: CCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCT-GG
EST: gi|17932241|gb|BM269201.1|BM269201
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
EST: gi|74232442|gb|DT640356.1|DT640356
EST:     CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAG                         GTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT
genomic: CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGT

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: 94

CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGTGAACATATTCCTTAGGTTATTTGGGAAGTGCTCGGAGAAGGCCCTTTGC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 58

CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGTGAACATATTCCTTAGGTTATTTGGGAAGTGCTCGGAGAAGGCCCTTTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGTGAACATATTCCTTAGGTTATTTGGGAAGTGCTCGGAGAAGGCCCTTTGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 87

CTCTTTCACTTTGTTCCTTGCCCAAGACATAGGTTGCCGAGgtactttcgt ... ccatccacagGTTTGATCCTGAAACGGGTCTGTTGACTGGTACCAAAGATGGTAATCTGGTGAACATATTCCTTAGGTTATTTGGGAAGTGCTCGGAGAAGGCCCTTTGC