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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggcctgttgcctttctctttactttgtcccgttcgtcgatttcaactaaagcttaggatgagggcgcggtgcgctcatagatgggtgtaatta...

Basic information

species Zea mays
transcript GRMZM5G832740_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G832740_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 2
GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggcctgttgcctttctctttactttgtccc--gttcgtcgatttcaactaaagcttaggatgagggcgcggtgcgctcatagatgggtgtaatta--
 ||||||| ||||||||||| ||||||||||||||| ||||||||||||||| |       |     | | |  ||| ||     |  | | |  |   | || |||  | | || |  ||  | |   | | ||| ||| ||||   
TCCTTCCATTGCAAGCACGGGAAGGCGTACCTCTTCAATAAGGTgtaagtggcctctccttcccgggcctcatcttgccctcgaatttttgttcgctcgtcaaactttaggt-agcgtacgccggg---agatatgtgtggaatttgg
















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:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|29544419|gb|CB604799.1|CB604799
EST:     GGCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGA
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGA
EST: gi|30031938|gb|CB833789.1|CB833789
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|149090255|gb|EE179558.2|EE179558
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|14203013|gb|BG836690.1|BG836690
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|29544063|gb|CB604443.1|CB604443
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|32909109|gb|CF013921.1|CF013921
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211513404|gb|FL378364.1|FL378364
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAGGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|116816600|gb|EC859352.1|EC859352
EST:     GCCTTCCANGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCA-GTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211349084|gb|FL422798.1|FL422798
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211514494|gb|FL430420.1|FL430420
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|29544546|gb|CB604926.1|CB604926
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|30031937|gb|CB833788.1|CB833788
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211046404|gb|FL436681.1|FL436681
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGMCCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211150622|gb|FL420950.1|FL420950
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|50327958|gb|CO523084.1|CO523084
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211094740|gb|FL379405.1|FL379405
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|149090254|gb|EE179557.2|EE179557
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211198966|gb|FL379005.1|FL379005
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|5847256|gb|AW000335.1|AW000335
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211403686|gb|FL424164.1|FL424164
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAG
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAG
EST: gi|211060747|gb|FL419541.1|FL419541
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|33942278|gb|CF348878.1|CF348878
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211084997|gb|FL399465.1|FL399465
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|211150629|gb|FL420957.1|FL420957
EST:     GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
EST: gi|5325164|gb|AI783355.1|AI783355
EST:     TCCAAGGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGT                         TGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT
genomic: TCCAAGGCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAAT

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: 44 (upstream exon), 47 (downstream exon)
Score: 117

GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 67

GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGG


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

GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 199

GCCTTCCAGTGCAAGCACGGCAAGGCGTACCTCTTCCATAAGGTgtaagtgggc ... ttatgcccagTGTCAACGTGACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGG