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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcctctccacccctccgcgtcccctctgccagacaaaaaaaatagagaggaaaatgggaaatttcttgttgtccccacggcggatgtacgcgtgcggtgtggctgatagcggtttctttccttggtgtttcgatttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT

Basic information

species Zea mays
transcript GRMZM5G832740_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G832740_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g49150.2 (Oryza sativa), 3'ss of exon 1
gttcctctccacc-cctccgcgtcccctctgccagacaaaaaaaatagagaggaaaatgggaaatttcttgtt--gtccccacggcggatgtacgcgtgcggtgtggctgatagcggtttctttccttggtgtttcgatttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
||||  |||  |  || || | |  | ||| |    |        |   |  |       |   | | |  ||  |    ||||||||||||  | | ||| | ||  | || |  | | ||||||           ||||||| ||| ||||||| ||||||||||| ||||||||||||||| |||||||
gttcgcctcttcagccccctcctttcttcttcttctcgttgttgttgttgttgttggctagctttgtttgattcggcgagcacggcggatgt--gggagcgat-tgtttcatggttgctgctttcc-----------atttcttgcagTCCTTCCATTGCAAGCACGGGAAGGCGTACCTCTTCAATAAGGT

upper sequence: GRMZM5G832740_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g49150.3 (Oryza sativa), 3'ss of exon 1
gttcctctccacc-cctccgcgtcccctctgccagacaaaaaaaatagagaggaaaatgggaaatttcttgtt--gtccccacggcggatgtacgcgtgcggtgtggctgatagcggtttctttccttggtgtttcgatttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT--------------------------------------------------------
||||  |||  |  || || | |  | ||| |    |        |   |  |       |   | | |  ||  |    ||||||||||||  | | ||| | ||  | || |  | | ||||||           ||||||| ||| ||||||| ||||||||||| ||||||||||||||| |||||||                                                        
gttcgcctcttcagccccctcctttcttcttcttctcgttgttgttgttgttgttggctagctttgtttgattcggcgagcacggcggatgt--gggagcgat-tgtttcatggttgctgctttcc-----------atttcttgcagTCCTTCCATTGCAAGCACGGGAAGGCGTACCTCTTCAATAAGGTGTAAGTGGCCTCTCCTTCCCGGGCCTCATCTTGCCCTCGAATTTTTGTTCGCTCGT
















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|211112095|gb|FL402628.1|FL402628
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211363300|gb|FL391103.1|FL391103
EST:     GCAAACACTGCRAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGC
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGC
EST: gi|29544419|gb|CB604799.1|CB604799
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GGCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|30031938|gb|CB833789.1|CB833789
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|149090255|gb|EE179558.2|EE179558
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|14203013|gb|BG836690.1|BG836690
EST:     CAAACACTGCAAGACCCACCCTCG-CGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: CAAACACTGCAAGACCCACC-TCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|29544063|gb|CB604443.1|CB604443
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|32909109|gb|CF013921.1|CF013921
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211513404|gb|FL378364.1|FL378364
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|116816600|gb|EC859352.1|EC859352
EST:     GCAAGCACTGCAAGACCCACCTCGGCGTTGCCAGCGACGTCATCTCCAAG                         GCCTTCCANGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCA-GTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211349084|gb|FL422798.1|FL422798
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211514494|gb|FL430420.1|FL430420
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|29544546|gb|CB604926.1|CB604926
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|30031937|gb|CB833788.1|CB833788
EST:     CGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: CGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211046404|gb|FL436681.1|FL436681
EST:     GGCGTTGCCAGCGACATCATYTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211150622|gb|FL420950.1|FL420950
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGC-AGCGACATCATCNCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|50327958|gb|CO523084.1|CO523084
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211094740|gb|FL379405.1|FL379405
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|149090254|gb|EE179557.2|EE179557
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211198966|gb|FL379005.1|FL379005
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|5847256|gb|AW000335.1|AW000335
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211403686|gb|FL424164.1|FL424164
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211060747|gb|FL419541.1|FL419541
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|33942278|gb|CF348878.1|CF348878
EST:     GCAAGCACTGTAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211084997|gb|FL399465.1|FL399465
EST:     GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
EST: gi|211150629|gb|FL420957.1|FL420957
EST:     CAAACACTGCAAGACCCCACCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
genomic: CAAACACTGCAAGA-CCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT

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), 49 (downstream exon)
Score: 118

GGCGATGGGGCGCCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 48

GGCGATGGGGCGCCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 70

GGCGATGGGGCGCCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

GGCGATGGGGCGCCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAACACTGCAAGACCCACCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcc ... tttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcgtgcggtgtggctgatagcggtttctttccttggtgtttcgatttcttccagGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT
            ggctgat  putative branch site (score: 181)
                                       tttcgatttcttcc  putative PPT
                        tttcttt  TA-rich tract