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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggcttcaatccttccataccttgtgtgcgtgcgcttccatgggttggttactgcaatctgctatacgatcaggaaggcagtaagcaactttgttgtttacactaaatggtcctcttctgtctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCCAGCATGAGCATCGTAGTTAAGGCACTCTCACCCCTTCTTCAACATAAAC

Basic information

species Zea mays
transcript GRMZM2G029530_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029530_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g33860.1 (Oryza sativa), 3'ss of exon 7
gtctggcttcaatccttccataccttgtgtgcgtgcgc-ttccatgggttggttactgcaatctgctatacgatcaggaaggcagtaagcaactttgttgtttacactaaatggtcctcttctgtctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCCAGCATGAGCATCGTAGTTAAGGCACTCTCACCCCTTCTTCAACATAAAC
||||| || |   |   |    | ||   |||    ||  ||  | |  |||| ||||      || |       || ||    |||| |||        |||   |  ||||||   | ||||| | |||||||| || || ||||||||||| ||||||||||| || ||||| |||||||| ||||||||||| || || ||||||||||| || ||||| || |||||||
gtctgcctccctcctcccttccctttaaatgcacaagcactctcttgtatggtcactgtgtggagcca-------agcaacatcgtaaccaaa------atttgagcccaatggtttccatctgtttattgcagCTCGCAGCGGTGGCGGCACTCTGTGTGCAATACGAGTCTGAGTTTAGACCAAGCATGAGCATTGTGGTCAAGGCACTCTCCCCTCTTCTCCAGCATAAAC

upper sequence: GRMZM2G029530_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
--gtctggcttcaatccttccataccttgtgtgcgtgcgcttccatgggttggttactgcaatctgctatacgatcaggaaggcagtaagcaactttgttgtttacactaaatggtcct-cttctgtctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCCAGCATGAGCATCGTAGTTAAGGCACTCTCACCCCTTCTTCAACATAAAC
   |||   |  | | ||  |    |||  ||||  || | |   ||    |  || ||     ||    | | || ||      |    | | ||| | ||| ||| |||  |  ||| ||  || | || ||||||||  ||||| ||||||||||| ||||| |||||| |||| ||||| || |  |||||||| || ||||| ||||||  ||| |||||  |   |    
gtatctatttctatttctcactcctcttaagtgcacgcacat--gtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgt-gcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG
















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|76935777|gb|DV174468.1|DV174468
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATTTGAATTTAGACCC
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
EST: gi|18649452|gb|BM498271.1|BM498271
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAAT
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAAT
EST: gi|89764339|gb|DY691183.1|DY691183
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
EST: gi|67043118|gb|CO469373.1|CO469373
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
EST: gi|211108272|gb|FL036813.1|FL036813
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
EST: gi|18383742|gb|BM416942.1|BM416942
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CATGCGGCTGTGGCGGCACTGTGTGTGCAATATGA
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGA
EST: gi|67032611|gb|CO461360.1|CO461360
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
EST: gi|18450374|gb|BM428652.1|BM428652
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CT-GCGGCTGTGGCGGC-CTGTGTGTGCAATATGAATCTGAATTTAGACCC
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
EST: gi|4827765|gb|AI668457.1|AI668457
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
EST: gi|18649205|gb|BM498009.1|BM498009
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CTTGCGGCTGTGGCGGCACTGTGTGTGCAATATG
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATG
EST: gi|78026567|gb|DV494954.1|DV494954
EST:     GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG                         CTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC
genomic: GTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCC

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: 44

GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCCAGCATGAGCATCGTAGTTAAGGCACTCTCACCCCTTCTTCAACATAAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 38

GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCCAGCATGAGCATCGTAGTTAAGGCACTCTCACCCCTTCTTCAACATAAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCCAGCATGAGCATCGTAGTTAAGGCACTCTCACCCCTTCTTCAACATAAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAGgtctggcttc ... tctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCCAGCATGAGCATCGTAGTTAAGGCACTCTCACCCCTTCTTCAACATAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcagtaagcaactttgttgtttacactaaatggtcctcttctgtctgttgcagCTTGCGGCTGTGGCGGCACTGTGTGTGCAATATGAATCTGAATTTAGACCCAGCATGAGCATCGTAGTTAAGGCACTCTCACCCCTTCTTCAACATAAAC
                         cactaaa  putative branch site (score: 56)
                                   tcctcttctgtctgtt  putative PPT
                  ttgttta  TA-rich tract