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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggtttcacatccacatcctttccatccttgcccattgtgctaaagaaagtttacaacttcgagaaaaatctggtcggttatgttatcttgattgagctttcttattttttttctag

Basic information

species Zea mays
transcript GRMZM2G002859_T01
intron # 6
splice site 5'
intron type U2

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|71307047|gb|DR789678.1|DR789678
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|149070323|gb|EE158722.2|EE158722
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATTTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|33091909|gb|CF051903.1|CF051903
EST:     GAAATTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|148986436|gb|EE030178.2|EE030178
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATTTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|40336986|gb|CK371056.1|CK371056
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|40335185|gb|CK369255.1|CK369255
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|60356623|gb|DN223596.1|DN223596
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
EST: gi|37380473|gb|CF627052.1|CF627052
EST:     GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG                         ATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT
genomic: GAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGT

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: 349

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 135

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAGgtctgatggt ... ttttttctagATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA