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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaactaataacagttactaattttacatatttcgccgtgggaatgcatgaaagggttttatgttgctgttctgtctgttacag

Basic information

species Zea mays
transcript GRMZM5G801369_T03
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G801369_T03 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 5'ss of exon 13
GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaactaataacagttactaattttacatatttcgccgtgggaatgcatgaaagggttttatgttgctgttctgtctg--ttacag----------
|||| ||| |||||||||| | |||||||||||||||||||||| ||   |    || ||   ||  |||  |  ||  |    |||||||||         |       | || | ||  |  ||           
GGCACGGCTGAGAATGGAAGAACACCATGGGAAGGGgtaagctagctctgatgtattcctcgcttctcat-ctgggcatttccgatgcatgaattctagacttaacaacatcctatatgaatcgcaaccatccgcaa
















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|56461966|gb|CK986264.1|CK986264
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|4621622|gb|AI612455.1|AI612455
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32838018|gb|CD977696.1|CD977696
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|78120790|gb|DV539174.1|DV539174
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32837052|gb|CD976730.1|CD976730
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|6021059|gb|AW065987.1|AW065987
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGNTCCAAACAAGGGTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|6601788|gb|AW256229.1|AW256229
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAANCAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|211502844|gb|FL437375.1|FL437375
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32917091|gb|CF021903.1|CF021903
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|211325390|gb|FL371043.1|FL371043
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|18164577|gb|BM334416.1|BM334416
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|50331568|gb|CO526694.1|CO526694
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32838737|gb|CD978418.1|CD978418
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32832999|gb|CD972677.1|CD972677
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|12973204|gb|BG268364.1|BG268364
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT

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: 50

GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACTGATGCTGAGAAAGCATATTACTTGGAGCACGGGATCACACCACCAAAAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 46

GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACTGATGCTGAGAAAGCATATTACTTGGAGCACGGGATCACACCACCAAAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 35

GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACTGATGCTGAGAAAGCATATTACTTGGAGCACGGGATCACACCACCAAAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACTGATGCTGAGAAAGCATATTACTTGGAGCACGGGATCACACCACCAAAAT