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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggagaatttagtaatagtcgatcctgtcctgtgtggttttcgccttcgcacatccgatatagtggtgtttgcccgtaaagttgcgcttaaatgaa...

Basic information

species Zea mays
transcript AC208327.4_FGT003
intron # 2
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|20811103|gb|BQ295581.1|BQ295581
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|78089597|gb|DV517971.1|DV517971
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|211516191|gb|FL166755.1|FL166755
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|26456410|gb|CA827993.1|CA827993
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|33467487|gb|CF244536.1|CF244536
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|148933097|gb|EC876730.2|EC876730
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|211466442|gb|FL172133.1|FL172133
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|19822069|gb|BQ048093.1|BQ048093
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|211516190|gb|FL166754.1|FL166754
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|26457087|gb|CA828670.1|CA828670
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT

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: 473

AAAACTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

AAAACTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 198

AAAACTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

AAAACTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT