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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaaatttgagtcctttatttaagttttattagtcttgtaacttaaattatgaccacttatagatagttgttttaaattacagGAATTCGAAGCTAACACACTTGCTACAAGACTCATTAA

Basic information

species Zea mays
transcript GRMZM2G400223_T03
intron # 8
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|5566690|gb|AI881706.1|AI881706
EST:     GGTGATGTCATATCCGCTCTTGCAACGAAGACCTCACATATACCCTTTAG                         GAATTCGAAGCTAACACACTTGCTACAAGACTCATTAA
genomic: GGTGATGTCATATCCGCTCTTGCAACAAAGACCTCACATATACCCTTTAGgtatttaaat ... taaattacagGAATTCGAAGCTAACACACTTGCTACAAGACTCATTAA




















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: 36 (upstream exon), 46 (downstream exon)
Score: 55

GAGAAAGATTGAAAGAAGCACAGAATATAAACAAATCACTTTCTGCACTTGGTGATGTCATATCCGCTCTTGCAACAAAGACCTCACATATACCCTTTAGgtatttaaat ... taaattacagGAATTCGAAGCTAACACACTTGCTACAAGACTCATTAA


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

GAGAAAGATTGAAAGAAGCACAGAATATAAACAAATCACTTTCTGCACTTGGTGATGTCATATCCGCTCTTGCAACAAAGACCTCACATATACCCTTTAGgtatttaaat ... taaattacagGAATTCGAAGCTAACACACTTGCTACAAGACTCATTAA


Block sizes: 49 (upstream exon), 17 (downstream exon)
Score: 4

GAGAAAGATTGAAAGAAGCACAGAATATAAACAAATCACTTTCTGCACTTGGTGATGTCATATCCGCTCTTGCAACAAAGACCTCACATATACCCTTTAGgtatttaaat ... taaattacagGAATTCGAAGCTAACACACTTGCTACAAGACTCATTAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 9

GAGAAAGATTGAAAGAAGCACAGAATATAAACAAATCACTTTCTGCACTTGGTGATGTCATATCCGCTCTTGCAACAAAGACCTCACATATACCCTTTAGgtatttaaat ... taaattacagGAATTCGAAGCTAACACACTTGCTACAAGACTCATTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtcttgtaacttaaattatgaccacttatagatagttgttttaaattacagGAATTCGAAGCTAACACACTTGCTACAAGACTCATTAA
       ttgtaac  putative branch site (score: 9)
                                       ttgtttt  putative PPT
                             ttatagatagttgttt  TA-rich tract