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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcccctctgtgcatgcagactgacatttttgcaactagttgactttggatctcatattcgtcattgtctgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTGCGCAATAACGTACAATTCCAAAACCTGCTTGGTTTGGTGCAGGCTAATC

Basic information

species Zea mays
transcript GRMZM2G105772_T01
intron # 7
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|6022682|gb|AW067610.1|AW067610
EST:     GACCAAATGCTAACCCTCTAGACCTCTTTCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
genomic: GACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
EST: gi|31364335|gb|CD448690.1|CD448690
EST:     CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTCCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
genomic: CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
EST: gi|148969759|gb|EE020640.2|EE020640
EST:     CTGCAGCTCCATCTGGACCCAATGCTACCCCTCTAGACCTCTTTCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAATCTTTGATGTTTT
genomic: CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTT-GATGTTTT
EST: gi|91876142|gb|EB406099.1|EB406099
EST:     CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
genomic: CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
EST: gi|78023202|gb|DV491589.1|DV491589
EST:     TGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
genomic: TGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
EST: gi|78118533|gb|DV536917.1|DV536917
EST:     TGCAGCTCCATCTGGGAC-AAATGCTAACCCTCTAGACCTCTTTCCCCA-                         TCTCTTCCGAAATGCTTCCGCCA-TGCTGGCACAGGAAACC
genomic: TGCAGCTCCATCTGG-ACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAA-TGCTTCCGCCAATGCTGGCACAGGAAACC
EST: gi|76011554|gb|DT938724.1|DT938724
EST:     TGCAGCTCCATCT-GACCCAAATGCTAACCCTCTAGACCTCTTTCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
genomic: TGCAGCTCCATCTGGA-CCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
EST: gi|149099558|gb|EE185596.2|EE185596
EST:     CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
genomic: CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
EST: gi|31363913|gb|CD448268.1|CD448268
EST:     CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTCCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
genomic: CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
EST: gi|148956696|gb|EC902566.2|EC902566
EST:     CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACA
genomic: CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACA
EST: gi|91054259|gb|EB164677.1|EB164677
EST:     CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAA                         TCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG
genomic: CTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTG

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: 215

TCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTGCGCAATAACGTACAATTCCAAAACCTGCTTGGTTTGGTGCAGGCTAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

TCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTGCGCAATAACGTACAATTCCAAAACCTGCTTGGTTTGGTGCAGGCTAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

TCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTGCGCAATAACGTACAATTCCAAAACCTGCTTGGTTTGGTGCAGGCTAATC


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 99

TCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTGGACCAAATGCTAACCCTCTAGACCTCTTTCCCCAAgtaactcccc ... tgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTGCGCAATAACGTACAATTCCAAAACCTGCTTGGTTTGGTGCAGGCTAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttgcaactagttgactttggatctcatattcgtcattgtctgaactgtagTCTCTTCCGAATGCTTCCGCCAATGCTGGCACAGGAAACCTTGATGTTTTGCGCAATAACGTACAATTCCAAAACCTGCTTGGTTTGGTGCAGGCTAATC
             agttgac  putative branch site (score: 99)
                            tcatatt  TA-rich tract