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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACTGGAGCAATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagctcttttgcctgtatctgtattttggttgtccaaccttccgtcgctgttggggttcttacaatttttttcccatcatggataaatctgttgc...

Basic information

species Zea mays
transcript GRMZM2G073054_T01
intron # 20
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|60347950|gb|DN214923.1|DN214923
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
EST: gi|60338294|gb|DN205267.1|DN205267
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
EST: gi|149040592|gb|EE046833.2|EE046833
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
EST: gi|78024920|gb|DV493307.1|DV493307
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATTGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
EST: gi|60394366|gb|DN227236.1|DN227236
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATTGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
EST: gi|4966932|gb|AI691970.1|AI691970
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATTGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
EST: gi|113702675|gb|EE680179.1|EE680179
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
EST: gi|91878000|gb|EB407957.1|EB407957
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
EST: gi|60345781|gb|DN212754.1|DN212754
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATTGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
EST: gi|211026372|gb|FL004586.1|FL004586
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATCGTTTTAGATTCTGACGATGG
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGG
EST: gi|166506299|gb|EG293636.1|EG293636
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGG
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGG
EST: gi|101386687|gb|EB815360.1|EB815360
EST:     ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAG                         ATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT
genomic: ATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGAT

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: 692

CATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACTGGAGCAATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGATCATGATGCCGAGTACTTCACTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

CATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACTGGAGCAATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGATCATGATGCCGAGTACTTCACTGCT


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 19

CATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACTGGAGCAATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGATCATGATGCCGAGTACTTCACTGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 272

CATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACTGGAGCAATAGCTATTTTGACTATCGCGTTGGTTGTTTCAAGCCTGGGAAGTACAAGgtatgcagct ... tccttgccagATCGTTTTAGATTCTGACGATGGCCTTTTCGGTGGATTTAGTCGGCTTGATCATGATGCCGAGTACTTCACTGCT