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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaaattctgcagctgtctcgcacccctgctatgcagtttaccgagttagcgttcccttcttgttgactgttattctgactttgttctttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATCTG

Basic information

species Zea mays
transcript GRMZM2G019812_T02
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|18180597|gb|BM381807.1|BM381807
EST:     TTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATT                         GTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATC
genomic: TTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATTgtgagcaaat ... tttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATC
EST: gi|148956071|gb|EC901822.2|EC901822
EST:     TCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATT                         GTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATC
genomic: TCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATTgtgagcaaat ... tttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATC
EST: gi|3157148|gb|AA979770.1|AA979770
EST:     TCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATT                         GTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATC
genomic: TCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATTgtgagcaaat ... tttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATC
EST: gi|9742960|gb|BE519108.1|BE519108
EST:     TCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATT                         GTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATC
genomic: TCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATTgtgagcaaat ... tttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATC

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: 48 (upstream exon), 47 (downstream exon)
Score: 129

GAGACATGAAGTTCAAACAAAACAAGTTCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATTgtgagcaaat ... tttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATCTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 172

GAGACATGAAGTTCAAACAAAACAAGTTCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATTgtgagcaaat ... tttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

GAGACATGAAGTTCAAACAAAACAAGTTCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATTgtgagcaaat ... tttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATCTG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 129

GAGACATGAAGTTCAAACAAAACAAGTTCTTGCCCCCCGATAAGCAAATCCTGACTGCGAACCCCGACATAAACATTgtgagcaaat ... tttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagttagcgttcccttcttgttgactgttattctgactttgttctttcgtgcagGTCGAGCTATGTGATGACGACGAATTCATTGTTTTGGCATGCGATGGCATCTG
                               ttctgac  putative branch site (score: 129)
                                     ctttgttctttcgt  CT-rich tract
                          tgttatt  TA-rich tract