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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactgcccactcttcaaactagacaccaaaataaaagggaccagtcttacatgcatgttttgttaatccctatgtttgggtgtcttag

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g47220.2 (Oryza sativa), 5'ss of exon 9
ATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactgcccactcttcaaactagacaccaaaataaaagggaccagtcttacatgcatgttttgttaatccctatgtttgggtgtcttag
||||||||||||||||||||||||||||||| || |||||||||||||||||||||||| ||||  |||| ||||| ||||||||||| |||||||||||||||| |  || | ||  ||  ||   ||    | | |||     ||  |  |   |  |||||     |   | | ||||||    ||| ||
ATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTGCAAGGGAAGTTACATCCGTGCCACCATACACAGAATATGTGTCAACTCGCTGgttagta--gcactctactcgcac---acgtggacacaaatc---ccttttctttgttaatgttgatcca---catgtgtttgaacatctcag
















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|60349468|gb|DN216441.1|DN216441
EST:     AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|8103639|gb|AW928260.1|AW928260
EST:     AGGGAAGTTTCATCATTGCCGCCATATACAGAATATGTCTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|211496286|gb|FL041698.1|FL041698
EST:     AGGGAAGTTTCATCATTGCCGCCATATACAGAATATGTCTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATATGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|32871065|gb|CF010747.1|CF010747
EST:     AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|32932540|gb|CF037352.1|CF037352
EST:     AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|31350422|gb|CD434779.1|CD434779
EST:     AGGGAAGTTTCATCATTGCCGCCATATACAGAATATGTCTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|47961778|gb|CN844487.1|CN844487
EST:     AGGGAAGTTTCATCATTGCCGCCATATACAGAATATGTCTCACCTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     AGGGAAGTTTCATCATTGCCGCCATATACAGAATATGTCTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|211496285|gb|FL041697.1|FL041697
EST:     AGGGAAGTTTCATCATTGCCGCCATATACAGAATATGTCTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: AGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
EST: gi|5932684|gb|AW057045.1|AW057045
EST:     CTCAACTCGCTG                         GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT
genomic: CTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGT

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), 47 (downstream exon)
Score: 259

ATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 172

ATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

ATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 206

ATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCGCTGgttagcactg ... ggtgtcttagGTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG