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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCCACTGGTCAAGTGGAGACACATGCTCCTGCGGGTGGCCCGACTTCATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagcatctgaggctcagatacaattaacagagctctattatcttgatcgtttcagtttgtagcttatgttaactggaaaccctaattgttgttgt...

Basic information

species Zea mays
transcript GRMZM2G018837_T01
intron # 8
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|32832550|gb|CD972228.1|CD972228
EST:     ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAG                         GTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
genomic: ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
EST: gi|45567963|gb|CK985834.1|CK985834
EST:     ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAG                         GTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
genomic: ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
EST: gi|32835258|gb|CD974936.1|CD974936
EST:     ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAG                         GTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
genomic: ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
EST: gi|78077795|gb|DV506224.1|DV506224
EST:     ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAG                         GTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
genomic: ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
EST: gi|60339880|gb|DN206853.1|DN206853
EST:     ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAG                         GTGGAACTGATTCTGCAGGGTATGGCATCGACCAAAGCGCAACACATCCAT
genomic: ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
EST: gi|211057558|gb|FL294381.1|FL294381
EST:     ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAG                         GTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
genomic: ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
EST: gi|211057555|gb|FL294378.1|FL294378
EST:     ATATCAACAATACTTCTCTTCGATGAGCATGCCAGGGCCTTCACCATCAG                         GTGGAACTGATTCTGCAGGGTATGGCATCGACCAAAGCGCAACACATCCAT
genomic: ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
EST: gi|32833736|gb|CD973414.1|CD973414
EST:     ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAG                         GTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
genomic: ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
EST: gi|32835640|gb|CD975318.1|CD975318
EST:     ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAG                         GTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT
genomic: ATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCAT

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: 121

GCATCCACTGGTCAAGTGGAGACACATGCTCCTGCGGGTGGCCCGACTTCATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCATCTCAGCTGCAGAGTTCATCCGCCAATGTCCAGGCACCATATGATGACAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

GCATCCACTGGTCAAGTGGAGACACATGCTCCTGCGGGTGGCCCGACTTCATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCATCTCAGCTGCAGAGTTCATCCGCCAATGTCCAGGCACCATATGATGACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

GCATCCACTGGTCAAGTGGAGACACATGCTCCTGCGGGTGGCCCGACTTCATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCATCTCAGCTGCAGAGTTCATCCGCCAATGTCCAGGCACCATATGATGACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

GCATCCACTGGTCAAGTGGAGACACATGCTCCTGCGGGTGGCCCGACTTCATATCAACAATACCTCTCTTCGATGAGCATGCCAGGGCCATCACCATCAGgtgagcagca ... tttttttcagGTGGAACTGATTCTGCAGGGTATGGCGTCGACCAAAGCGCAACACATCCATCTCAGCTGCAGAGTTCATCCGCCAATGTCCAGGCACCATATGATGACAC