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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcatttcccctgtgctttgcctctcttatattcatatgaagtgcaaaaggcatttccttgaacagcatggcgacagggcaatgcataacatttttt...

Basic information

species Zea mays
transcript GRMZM2G059039_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059039_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g20930.1 (Oryza sativa), 5'ss of exon 9
AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcatttcc--cctgtgctttgcctctcttatattcatatgaagtgcaaaaggcatttccttg-aacagcatggcgacagggcaa-tgcataacatttttt
||||| | |||    |||||||||||||| || |||||||| |||||||||||||  ||||| ||||||||| | |    | ||| | |||   |   |   ||  |   ||   ||  |     ||| ||  ||    ||   | || ||||  |  | |||  ||   
AGAGGGGGATCGAGCAGCAAGTTCCTCAACTATTTCGTTAAGCAAATTGTTCCAGTTTTTGACAAGgtaatcttctttatcttgtacattggtccctgtgctttgttggaaaaaacagtaaatgcttctttttaattatattatg-catggcagctctacaaccctt---
















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|60338080|gb|DN205053.1|DN205053
EST:     GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG                         ATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCA
genomic: GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcattt ... catattttagATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCA
EST: gi|32933981|gb|CF038793.1|CF038793
EST:     GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG                         ATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCA
genomic: GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcattt ... catattttagATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCA
EST: gi|31356580|gb|CD440937.1|CD440937
EST:     GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG                         ATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCA
genomic: GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcattt ... catattttagATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCA
EST: gi|60398546|gb|DN231362.1|DN231362
EST:     GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG                         ATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCA
genomic: GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcattt ... catattttagATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCA
EST: gi|31358588|gb|CD442945.1|CD442945
EST:     GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAG                         ATTCCTGAAGAAAAGAAACTGCATTTGCTAAAGACTATTGCTTCAAGTTCA
genomic: GCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcattt ... catattttagATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCA

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), 48 (downstream exon)
Score: 322

AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcattt ... catattttagATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCACCATATGCTGCAGCACAAGATTCACGTCAGCTGCTTCCATCTGTTGTTC


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 118

AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcattt ... catattttagATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCACCATATGCTGCAGCACAAGATTCACGTCAGCTGCTTCCATCTGTTGTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 239

AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcattt ... catattttagATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCACCATATGCTGCAGCACAAGATTCACGTCAGCTGCTTCCATCTGTTGTTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 175

AGAGGAGCATCAGCAAGCAAGTTCCTCAATTACTTCGTTAAACAAATTGTTCCAGCATTTGAGAAGgtaatcattt ... catattttagATTCCTGAAGAAAAGAAACTGGATTTGCTAAAGACTATTGCTTCAAGTTCACCATATGCTGCAGCACAAGATTCACGTCAGCTGCTTCCATCTGTTGTTC