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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCTCCCCACCTGCTCCGCGCCTGCTCATCCGCCTCTTATACCATCGCTCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctattccactttctcgtctctctttttgtaacttcgttttcagttcagcgccggatgttcgtcgttctggcacgaggacgtaccacttgtgctgt...

Basic information

species Zea mays
transcript GRMZM2G460078_T02
intron # 1
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|78111750|gb|DV530147.1|DV530147
EST:     CGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: CGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
EST: gi|91049611|gb|EB160029.1|EB160029
EST:     TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
EST: gi|211025828|gb|FK982703.1|FK982703
EST:     ACTTCACCTCTTCTGCTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: ACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
EST: gi|211025826|gb|FK982701.1|FK982701
EST:     TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
EST: gi|211025831|gb|FK982706.1|FK982706
EST:     ACTTCACCTCTTCTGCTTCCTTCTCCCCAG                         CATACAGGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAA
genomic: ACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACA-GTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAA
EST: gi|71434528|gb|DR815578.1|DR815578
EST:     CTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: CTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
EST: gi|71332183|gb|DR803010.1|DR803010
EST:     TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
EST: gi|211025829|gb|FK982704.1|FK982704
EST:     TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
EST: gi|93012882|gb|EB638402.1|EB638402
EST:     GCTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: GCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
EST: gi|148961982|gb|EE012780.2|EE012780
EST:     TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: TCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
EST: gi|211025830|gb|FK982705.1|FK982705
EST:     ACTTCACCTCTTCTGCTTCCTTCTCCCCAG                         CATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG
genomic: ACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAG

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), 47 (downstream exon)
Score: 132

TCTTCTCCCCACCTGCTCCGCGCCTGCTCATCCGCCTCTTATACCATCGCTCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAGTCCTTAGGCATGGCTCAGCAGATAGTGTCCGTGCTGTCATAAGAGCTAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 209

TCTTCTCCCCACCTGCTCCGCGCCTGCTCATCCGCCTCTTATACCATCGCTCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAGTCCTTAGGCATGGCTCAGCAGATAGTGTCCGTGCTGTCATAAGAGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

TCTTCTCCCCACCTGCTCCGCGCCTGCTCATCCGCCTCTTATACCATCGCTCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAGTCCTTAGGCATGGCTCAGCAGATAGTGTCCGTGCTGTCATAAGAGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 804

TCTTCTCCCCACCTGCTCCGCGCCTGCTCATCCGCCTCTTATACCATCGCTCTCGCTCGCCTCCGACGCCACTTCACCTCTTCTGCTTCCTTCTCCCCAGgtcggctatt ... cgttctttagCATACAGTGCCAGACAGGATACCCACACATTCATGGAGGTGGTTCAAGAAGTCCTTAGGCATGGCTCAGCAGATAGTGTCCGTGCTGTCATAAGAGCTAA