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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagtccactagcttatccagcagaacttggtagcttacataaacagtttcctatatgttactaacaatatggtgtttatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG

Basic information

species Zea mays
transcript GRMZM2G351160_T01
intron # 3
splice site 3'
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|149069091|gb|EE157818.2|EE157818
EST:     GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCG                         TTTAGGTGATTTCTGGATGCTAGACACTG
genomic: GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG
EST: gi|78106677|gb|DV525095.1|DV525095
EST:     GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCG                         TTTAGGTGATTTCTGGATGCTAGACACTG
genomic: GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG
EST: gi|60348204|gb|DN215177.1|DN215177
EST:     GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCG                         TTTAGGTGATTTCTGGATGCTAGACACTG
genomic: GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG
EST: gi|76020393|gb|DT947563.1|DT947563
EST:     GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCG                         TTTAGGTGATTTCTGGATGCTAGACACTG
genomic: GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG
EST: gi|78114121|gb|DV532510.1|DV532510
EST:     GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCG                         TTTAGGTGATTTCTGGATGCTAGACACTG
genomic: GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG
EST: gi|148938635|gb|EC882966.2|EC882966
EST:     GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCG                         TTTAGGTGATTTCTGGATGCTAGACACTG
genomic: GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG
EST: gi|89756288|gb|DY686365.1|DY686365
EST:     GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCG                         TTTAGGTGATTTCTGGATGCTAGACACTG
genomic: GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG
EST: gi|148938619|gb|EC882949.2|EC882949
EST:     GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCG                         TTTAGGTGATTTCTGGATGCTAGACACTG
genomic: GTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG

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: 39 (upstream exon), 29 (downstream exon)
Score: 103

GGTCGGATGGGCAGGCCGGCCCAAGCCCAAGGGCTTTTCACATAGCTGTTGTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG


Block sizes: 48 (upstream exon), 29 (downstream exon)
Score: 66

GGTCGGATGGGCAGGCCGGCCCAAGCCCAAGGGCTTTTCACATAGCTGTTGTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

GGTCGGATGGGCAGGCCGGCCCAAGCCCAAGGGCTTTTCACATAGCTGTTGTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG


Block sizes: 47 (upstream exon), 31 (downstream exon)
Score: 93

GGTCGGATGGGCAGGCCGGCCCAAGCCCAAGGGCTTTTCACATAGCTGTTGTCATTGACTGCAACATGTTCATCTTTGGTGGCCGATCTGGGGGCAAGCGgtatgcagtc ... tatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttacataaacagtttcctatatgttactaacaatatggtgtttatctcacagTTTAGGTGATTTCTGGATGCTAGACACTG
                           tactaac  putative branch site (score: 93)
                                           tttatctc  putative PPT
                    tatatgtta  TA-rich tract