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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcatttcttgtgccattttacatgttttgtgataaacttctcatttttatatagaagaatatcatgaacttgaataatcatgtttcctccccactttgtctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAGGCTATCTCACATACACCGACTGTCATCGATCTATATTCAGTAAAG

Basic information

species Zea mays
transcript GRMZM2G047093_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047093_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g43030.1 (Oryza sativa), 3'ss of exon 13
gtctgcatt-----tcttgtgccattttacatgttt---tgtgataaacttctcatttttatatagaagaatatcatgaacttgaataatcatgtttcctccccactttgtctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAGGCTATCTCACATACACCGACTGTCATCGATCTATATTCAGTAAAG
||  |||||       | |||     || || | |    | | | ||     | |||  | |        || |  |||| |   ||  |||  |||  | | ||  |||  | ||||||||||| ||||||||||| || ||||| |||||| |  ||||||| ||||||||||| ||||| || || ||||| || ||| |||| ||| |||||
gttagcattgagcacttcgtgtttccttgcaagctaaaattttagaattccttaattgcttttattttttatcttttgaattcacatggtca-atttttttcacatgttgaatgatgcagCACTATGACAGAAGAGGCCAGTATGATATTGCTCTAGATAAAATTGATGAGGCTATTTCACACACGCCAACTGTAATTGATTTATACTCAATAAAG
















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|22490182|gb|BU050105.1|BU050105
EST:     AGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAG                         C-CTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAG
genomic: AGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAGgtctgcattt ... tctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAG
EST: gi|19057925|gb|BM736592.1|BM736592
EST:     AGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAG                         CACTACGACAGAAGAGGCCAATATGACATTGCTT-GAATAAAATCGATGAG
genomic: AGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAGgtctgcattt ... tctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAG
EST: gi|18963332|gb|BM660375.1|BM660375
EST:     AGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAG                         CACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAG
genomic: AGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAGgtctgcattt ... tctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAG
EST: gi|31349081|gb|CD433438.1|CD433438
EST:     AGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAG                         CACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAG
genomic: AGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAGgtctgcattt ... tctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAG

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: 163

TCCACAGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAGgtctgcattt ... tctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAGGCTATCTCACATACACCGACTGTCATCGATCTATATTCAGTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

TCCACAGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAGgtctgcattt ... tctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAGGCTATCTCACATACACCGACTGTCATCGATCTATATTCAGTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 148

TCCACAGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAGgtctgcattt ... tctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAGGCTATCTCACATACACCGACTGTCATCGATCTATATTCAGTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

TCCACAGAAGGAGCCTCCTTCCACACTGTTGTGGACCCTGTTTTTGATTTCTCAGgtctgcattt ... tctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAGGCTATCTCACATACACCGACTGTCATCGATCTATATTCAGTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaatatcatgaacttgaataatcatgtttcctccccactttgtctaatgcagCACTACGACAGAAGAGGGCAATATGACATTGCTTTGAATAAAATCGATGAGGCTATCTCACATACACCGACTGTCATCGATCTATATTCAGTAAAG
                                            gtctaat  putative branch site (score: 141)
                           tgtttcctccccactt  CT-rich tract
                ttgaataat  TA-rich tract