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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGCCATCGTAGATGGTGGAGCCCTTCCAGGATTTATAAATTTGGTGAGGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatctgaaatttgacttgtcaaaagcgttcagccatatcttttgtctacttgcattttcatatcacctcaattcgaattcatttggcag

Basic information

species Zea mays
transcript GRMZM2G165692_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165692_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g06470.1 (Oryza sativa), 5'ss of exon 10
AGTTGCCATCGTAGATGGTGGAGCCCTTCCAGGATTTATAAATTTGGTGAGGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaa-------------------tctgaaatttgacttgtcaaaagcgttcagcc------------------atatcttttgtctactt-------gcattttcatatcacctcaattcgaattcatttg-gcag
||| || ||||||||||||||||||||||||||||||||| | ||||| ||||| || ||| |||| | || | ||||| ||||||||||| |||||||| ||||| ||| || ||| | |||| | | || || ||| | || ||||| || |||| || | |||| ||||| ||||
AGTCGCTATCGTAGATGGTGGAGCCCTTCCAGGATTTATACACTTGGTCAGGTCTGCTGATGTAGATACCGCAGGGCTTGGTCTTCAGTTCCTAGAACTGgtgaggaaatctttaccatattagctatctctgtttcattcctccaacggtattcacctcacaagcagagttgctgaacatgttctgtttctttcttggatacatttggatctcactggaaattgaatacatttttgcag
















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|78080887|gb|DV509299.1|DV509299
EST:     GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTG                         GTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
genomic: GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
EST: gi|211295564|gb|FL447040.1|FL447040
EST:     GGTCAGCCGATATAGAGAGCGCGAGACTTGGGCTTCAGTTCCTGGAACTG                         GTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
genomic: GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
EST: gi|116815561|gb|EC858241.1|EC858241
EST:     GGTCAGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTG                         GTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAAGCTCGTGGAGACAGA
genomic: GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAA-GCTCGTGGAGACAGA
EST: gi|149013735|gb|EE043193.2|EE043193
EST:     GGTCGGCCGATATAGAGAGTGGGAGACTTGGGCTTCAGTTCCTGGAACTG                         GTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
genomic: GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
EST: gi|86467944|gb|DY234314.1|DY234314
EST:     GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTG                         GTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
genomic: GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
EST: gi|33097676|gb|CF057636.1|CF057636
EST:     GTCAGCCGATATAGAGAGTGCGAGACTTGGGCTTCCAGTTCCTGGAACTG                         GTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
genomic: GTCGGCCGATATAGAGAGTGCGAGACTTGGGCTT-CAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
EST: gi|37394069|gb|CF634304.1|CF634304
EST:     GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTG                         GTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
genomic: GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
EST: gi|60395305|gb|DN228174.1|DN228174
EST:     GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTG                         GTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
genomic: GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
EST: gi|148969107|gb|EE019842.2|EE019842
EST:     GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTG                         GTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG
genomic: GGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAG

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: 39

AGTTGCCATCGTAGATGGTGGAGCCCTTCCAGGATTTATAAATTTGGTGAGGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAGGACGGCATTGAGGCCATGGAGAGGTTCCAGTTCCATGAGAACGAGATGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 133

AGTTGCCATCGTAGATGGTGGAGCCCTTCCAGGATTTATAAATTTGGTGAGGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAGGACGGCATTGAGGCCATGGAGAGGTTCCAGTTCCATGAGAACGAGATGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 196

AGTTGCCATCGTAGATGGTGGAGCCCTTCCAGGATTTATAAATTTGGTGAGGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAGGACGGCATTGAGGCCATGGAGAGGTTCCAGTTCCATGAGAACGAGATGA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 44

AGTTGCCATCGTAGATGGTGGAGCCCTTCCAGGATTTATAAATTTGGTGAGGTCGGCCGATATAGAGAGTGCGAGACTTGGGCTTCAGTTCCTGGAACTGgtaaggaatc ... catttggcagGTGATGAGAGGATACCCTGACAGCCAGGGCCCAAAGCTCGTGGAGACAGAGGACGGCATTGAGGCCATGGAGAGGTTCCAGTTCCATGAGAACGAGATGA