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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaatcacgattgtttgttgactgtgtgaggccgtaaaaattgagatgtatttttaatatttttgtaatgctaaccatgtcaaatatgtctacacggttggatgaagTTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACGCCATGCTTTG

Basic information

species Zea mays
transcript GRMZM5G873291_T01
intron # 1
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|211497295|gb|FL313407.1|FL313407
EST:     GGACGCTCCCCATGCCTTGACGGCTTGACCTCCGATGGAGAGGAAGCAAG                         TTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACG
genomic: GGACGCTCCCCATGCCTTGACGGCTTGACCTCCGATGGAGAGGAAGCAAGgtgagaaatc ... ttggatgaagTTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACG
EST: gi|211050416|gb|FL364290.1|FL364290
EST:     GGACGCTCCCCATGCCTTGACGGCTTGACCTCCGATGGAGAGGAAGCAAG                         TTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACGCCATGCT
genomic: GGACGCTCCCCATGCCTTGACGGCTTGACCTCCGATGGAGAGGAAGCAAGgtgagaaatc ... ttggatgaagTTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACGCCATGCT

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: 44 (upstream exon), 49 (downstream exon)
Score: 14

CAGCCTCTGCACTACCGTCCAAGTCAAGTCGCTGTATCACCTTAGCCCATGGACGCTCCCCATGCCTTGACGGCTTGACCTCCGATGGAGAGGAAGCAAGgtgagaaatc ... ttggatgaagTTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACGCCATGCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 16

CAGCCTCTGCACTACCGTCCAAGTCAAGTCGCTGTATCACCTTAGCCCATGGACGCTCCCCATGCCTTGACGGCTTGACCTCCGATGGAGAGGAAGCAAGgtgagaaatc ... ttggatgaagTTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACGCCATGCTTTG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 17

CAGCCTCTGCACTACCGTCCAAGTCAAGTCGCTGTATCACCTTAGCCCATGGACGCTCCCCATGCCTTGACGGCTTGACCTCCGATGGAGAGGAAGCAAGgtgagaaatc ... ttggatgaagTTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACGCCATGCTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 18

CAGCCTCTGCACTACCGTCCAAGTCAAGTCGCTGTATCACCTTAGCCCATGGACGCTCCCCATGCCTTGACGGCTTGACCTCCGATGGAGAGGAAGCAAGgtgagaaatc ... ttggatgaagTTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACGCCATGCTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatatttttgtaatgctaaccatgtcaaatatgtctacacggttggatgaagTTGTACTGCTGTACCAGTTCACTGTATTTGTAGACTACACTACGCCATGCTTTG
                tgctaac  putative branch site (score: 18)
     tatttttgtaat  TA-rich tract