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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAATCAAATACGAGATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttctgataattttcttgcaatgtctagcttgcagatatttaatttaagttgtctttgacggctaaacagatcattatgtatagttatgtaactgctacaatttatcctgcacaatgccgattaatgttgatgcttctgcattgtgctgtgtaacccgcaaaccatatgaacactgattttgtttatgcag

Basic information

species Zea mays
transcript GRMZM2G305254_T06
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G305254_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 5'ss of exon 12
GTCAATCAAATACGAGATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttctgataattttcttgcaatgtctagcttg-cagatatttaatttaagttgtctttgacggctaaacagatcattatgtatagttatgtaactgctacaatttatcctgcacaatgccgattaatgttgatgcttctgcattgtgctgtgtaacccgcaaaccatatgaacactgattttgtttatgcag
|| ||||||||  |||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||| || |   | | |||| || ||   |   |  || | || ||| |   |  | |    |||  |   | || | | ||  ||| |   | | |||  |                                                                                          
GTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCTTTTAGCCTGCCCCAGgtgcatttccgaca---tccatgcagtgcctcattaatcttatttatagttttatacgcttctc---gctccatcaagcactttttaccgtt-taacatttctatta------------------------------------------------------------------------------------------

upper sequence: GRMZM2G305254_T04 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G03660.1 (Glycine max), 5'ss of exon 13
GTCAATCAAATACGAGATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttctgataattttcttgcaatgtctagcttgcagatatttaatttaagttgtctttgacggctaaacagatcattatgtatagttatgtaactgctacaatttatcctgcacaatgccgattaatgttgatgcttctgcattgtgctgtgtaacccgcaaaccatatgaacactgattttgtttatgcag
||||||||||| |||||||| ||||| ||||||||  || |||| ||||| |||||||| || || ||   | ||   |  ||      |||  |  |  ||     | ||||||||    |   ||  || |  |    | |     | | | | | | | |    |  |  ||                                                                                       
GTCAATCAAATCCGAGATTCATTGGCTGTTATGGGTGACAACAGTACTGCCTTTAGCTTACCGCAAgtatgtgtcccttggtt------caaaattcaaatt----ctctttaatttcttatcctttctactgtaatttgggtttcattatctggatttctgatatatggagcttt--------------------------------------------------------------------------------------
















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|18963438|gb|BM660435.1|BM660435
EST:     ATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAG                         CCACATCTTCAAAGAACAAAATTATGTGATATGGAGGACAAAGAGCTTGAA
genomic: ATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttct ... gtttatgcagCCACATCTTCAAAGAACAAAATTATGTGATATGGAGGACAAAGAGCTTGAA
EST: gi|19057930|gb|BM736597.1|BM736597
EST:     ATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAG                         CCACATCTTCAAAG
genomic: ATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttct ... gtttatgcagCCACATCTTCAAAG
EST: gi|160481497|gb|EY254329.1|EY254329
EST:     ATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAG                         CCACATCTTCAAAGAACAAAATTA
genomic: ATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttct ... gtttatgcagCCACATCTTCAAAGAACAAAATTA
EST: gi|18963930|gb|BM660710.1|BM660710
EST:     ATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAG                         CCACATCTTCAAAGAACAAAATTATGTGATATGGAGGACAAAGAGCTTGAA
genomic: ATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttct ... gtttatgcagCCACATCTTCAAAGAACAAAATTATGTGATATGGAGGACAAAGAGCTTGAA

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: 46 (upstream exon), 39 (downstream exon)
Score: 33

GTCAATCAAATACGAGATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttct ... gtttatgcagCCACATCTTCAAAGAACAAAATTATGTGATATGGAGGACAAAGAGCTTGAACCCTTATATGTAAAACGGCGGGAGCAACTAAAGCAGCTTGTTTCGTCCA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 36

GTCAATCAAATACGAGATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttct ... gtttatgcagCCACATCTTCAAAGAACAAAATTATGTGATATGGAGGACAAAGAGCTTGAACCCTTATATGTAAAACGGCGGGAGCAACTAAAGCAGCTTGTTTCGTCCA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 35

GTCAATCAAATACGAGATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttct ... gtttatgcagCCACATCTTCAAAGAACAAAATTATGTGATATGGAGGACAAAGAGCTTGAACCCTTATATGTAAAACGGCGGGAGCAACTAAAGCAGCTTGTTTCGTCCA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 30

GTCAATCAAATACGAGATTCTTTGGCAGTTATGGGCAACCACAGCACTGCTTTTAGCTTGCCCCAGgtgcatttct ... gtttatgcagCCACATCTTCAAAGAACAAAATTATGTGATATGGAGGACAAAGAGCTTGAACCCTTATATGTAAAACGGCGGGAGCAACTAAAGCAGCTTGTTTCGTCCA