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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctattctttggtgcaatacattttatctgctcatagtcatatgtagtgcttcgttgttcttgtggctaaattggatttaaacttctttttcag

Basic information

species Zea mays
transcript GRMZM2G114220_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114220_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g48770.1 (Oryza sativa), 5'ss of exon 3
TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctattctttggtgcaatacattttatctgctcatagtcatatgtagtgcttcgttgttcttgtggctaaattggatttaaacttctttttcag-------------------
||||| |  |||||||  |||||||| |     |||||||||||||||||||||||||||||||| || ||||| ||||||| ||  ||    ||||  |  |||  |    ||   | |  | | |  |  | | |  |      |  | || ||  |||    | ||||||                      
TTTTATGCAGGATATGGCTACCATGGGAGTAACTTTGAGCAAACATACCGTTGTTATCCAGCATCTTTCTTTGACAAGgtatccttctcccctgtgctgt-tattgaaatatctagcattgttttatccttttacatgatgaactggatttaactgtcttttttttccttttttttttttgcttcatttcttcag
















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|76909136|gb|DV163240.1|DV163240
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392498|gb|FL156787.1|FL156787
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAG-CGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392504|gb|FL156793.1|FL156793
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211395124|gb|FL156801.1|FL156801
EST:     ACTCGTTTGAGCAAACATACCGTTGGTATGCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211389877|gb|FL156782.1|FL156782
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAG-CGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392507|gb|FL156796.1|FL156796
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|91873355|gb|EB403312.1|EB403312
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|14242735|gb|BG840580.2|BG840580
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392505|gb|FL156794.1|FL156794
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|71417924|gb|DR804257.1|DR804257
EST:     ACTCGTCTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|50338446|gb|CO533572.1|CO533572
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392501|gb|FL156790.1|FL156790
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAVCATCGTTTTTTGATAAG                         CCMCACCTGGAAGGCGGKGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211389876|gb|FL156781.1|FL156781
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAG-CGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392496|gb|FL156785.1|FL156785
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|93015584|gb|EB641104.1|EB641104
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211389879|gb|FL156784.1|FL156784
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAG-CGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|32862738|gb|CF002420.1|CF002420
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392502|gb|FL156791.1|FL156791
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|91049005|gb|EB159423.1|EB159423
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|6637070|gb|AW261342.1|AW261342
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGCGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211395123|gb|FL156800.1|FL156800
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392503|gb|FL156792.1|FL156792
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392499|gb|FL156788.1|FL156788
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392510|gb|FL156799.1|FL156799
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|213183590|gb|FM196389.1|FM196389
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|32859779|gb|CD999460.1|CD999460
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG

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: 85

TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 96

TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

TTTTACGGGGGATATGCTTACCATGGCAACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG