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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTAGTCCCTGTCTCCTTCCCTCTAAACCCGCACCCGCAGCAGCGCCGCTAGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcccggccttctttcaagccccgacctagggtttctgcctgtttgttcagattttgttggttcgatctcaggcggctgtttcccgaag

Basic information

species Zea mays
transcript GRMZM2G139643_T04
intron # 1
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|101402086|gb|EB822652.1|EB822652
EST:     AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTG                         TTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
genomic: AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
EST: gi|50336822|gb|CO531948.1|CO531948
EST:     AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTG                         TTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
genomic: AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
EST: gi|76014054|gb|DT941224.1|DT941224
EST:     AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCC--G                         --T---GTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
genomic: AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
EST: gi|71417068|gb|DR803915.1|DR803915
EST:     AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTG                         TTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
genomic: AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
EST: gi|211508855|gb|FL158319.1|FL158319
EST:     AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTTCGTG                         TTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
genomic: AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
EST: gi|76282448|gb|DV022016.1|DV022016
EST:     AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTG                         TTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
genomic: AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
EST: gi|71768840|gb|DR966777.1|DR966777
EST:     AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTG                         TTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
genomic: AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
EST: gi|71446122|gb|DR827172.1|DR827172
EST:     AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTG                         TTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT
genomic: AGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGT

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: 47 (upstream exon), 49 (downstream exon)
Score: 92

TCTAGTCCCTGTCTCCTTCCCTCTAAACCCGCACCCGCAGCAGCGCCGCTAGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGTACGACGAGGAGGTCGACGAAGAGGAGGGACACCCCGGGAGGCGGGTAGG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 21

TCTAGTCCCTGTCTCCTTCCCTCTAAACCCGCACCCGCAGCAGCGCCGCTAGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGTACGACGAGGAGGTCGACGAAGAGGAGGGACACCCCGGGAGGCGGGTAGG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 11

TCTAGTCCCTGTCTCCTTCCCTCTAAACCCGCACCCGCAGCAGCGCCGCTAGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGTACGACGAGGAGGTCGACGAAGAGGAGGGACACCCCGGGAGGCGGGTAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 66

TCTAGTCCCTGTCTCCTTCCCTCTAAACCCGCACCCGCAGCAGCGCCGCTAGGGTTTGCTCAGGCCCCGAACCCCACCCTTGGATTGCTCTGATTCCGTGgtaatcagcc ... tttcccgaagTTTGCAGTATGGCGGGGTACCCGGAGGACAACCAGCACGAGTTGAACGGGTACGACGAGGAGGTCGACGAAGAGGAGGGACACCCCGGGAGGCGGGTAGG