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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacatctgttgcattggtctgtttttttgttgatttgtaaatctggtgacgaaaatgttcacgttatttgggactttttgagtattaaccctgctattcttcattctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGACACCCCTACCCAACTTGGGAACCAATAGTTTGTCACCTCCACCTTTGAGT

Basic information

species Zea mays
transcript GRMZM2G156800_T01
intron # 10
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|211137994|gb|FL439623.1|FL439623
EST:     AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG                         TGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
genomic: AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
EST: gi|33094498|gb|CF054492.1|CF054492
EST:     AAAGTAACCTGGAAAAGTGATTCATATATGAGAGGCAAACATGCAAATGG                         TGAAACAAACAGCGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
genomic: AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
EST: gi|71323591|gb|DR798464.1|DR798464
EST:     AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG                         TGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
genomic: AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
EST: gi|60359314|gb|DN226287.1|DN226287
EST:     AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG                         TGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
genomic: AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
EST: gi|33095640|gb|CF055634.1|CF055634
EST:     AAAGTAACCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG                         TGAAACAAACAGCGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGGTGAC
genomic: AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
EST: gi|71427641|gb|DR808691.1|DR808691
EST:     AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG                         TGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
genomic: AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
EST: gi|148955653|gb|EC901325.2|EC901325
EST:     AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG                         TGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
genomic: AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
EST: gi|60345120|gb|DN212093.1|DN212093
EST:     AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG                         TGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGA
genomic: AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGA
EST: gi|50338067|gb|CO533193.1|CO533193
EST:     AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG                         TGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
genomic: AAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
EST: gi|78023372|gb|DV491759.1|DV491759
EST:     GTGATTCATATATGAGAGGGAAACATGCAAATGG                         TGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC
genomic: GTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGAC

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), 45 (downstream exon)
Score: 29

GATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGACACCCCTACCCAACTTGGGAACCAATAGTTTGTCACCTCCACCTTTGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 29

GATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGACACCCCTACCCAACTTGGGAACCAATAGTTTGTCACCTCCACCTTTGAGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 17

GATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGACACCCCTACCCAACTTGGGAACCAATAGTTTGTCACCTCCACCTTTGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 15

GATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGGgtgagtacat ... attctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGACACCCCTACCCAACTTGGGAACCAATAGTTTGTCACCTCCACCTTTGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacgttatttgggactttttgagtattaaccctgctattcttcattctgatagTGAAACAAGCAGTGCTCGGTCGTCAGAGTCATTGGCTTATCGGTTGATGACACCCCTACCCAACTTGGGAACCAATAGTTTGTCACCTCCACCTTTGAGT
                         tattaac  putative branch site (score: 15)
                                    ctattcttcattct  putative PPT
                 tttttgagtattaa  TA-rich tract