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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCCGCAAGCCAAAACCCTAGCAAGCAAACCACCGGAGCAGCGGCGCTCGCGCGGGCGGAGCCATGGCGGACGACGATTACAACGAAATCGACATGGGgttcgactctccctcatccttcccccctctctggtgcctgtgtcgcctggccatgcaatggttataggagcatcattaggttttatttgtagatatgtag...

Basic information

species Zea mays
transcript GRMZM2G013600_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013600_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g38960.1 (Oryza sativa), 5'ss of exon 1
------GCAGCCGCAAGCCAAAACCCTAGCAAGCA-AACCACCGGAGCAGCGGCGCTCGCGCGGGCGGAGCCATGGCGGACGACGATTACAACGAAATCGACATGGGgttcgactctccctc-atccttcccccctctctggtgcctgtgtcgcctggccatgcaatggttata-ggagcatcattaggttttatttgtagatatgtag
      || ||||   | | |||||||||| |    | |  |||||      |       ||||  | |||||||||||||||||| |||||||| || ||||||||||| | ||  | ||| |   |  | | |||||| || | | |  ||  ||  ||||  |     ||   | |  ||  ||||  |    |||    ||    
CGCTTGGCCGCCGTGCGGCGAAACCCTAGCGATTGTAGCGGCCGGAATCAGAG-------GCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgccttactctctactatctcactctctctagtcctttttccgtatgatcatgggaatccaatctagggtttcgataggcatcgcctgttctaataa--
















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|211132168|gb|FL066405.1|FL066405
EST:     CGCGCGGGCGGA--SATGGC-GACGACGATTACAACGAAATCGACATGGG                         CTATGAGGATGAGCCTCCAGAACCTGAGATTGAG
genomic: CGCGCGGGCGGAGCCATGGCGGACGACGATTACAACGAAATCGACATGGGgttcgactct ... tgttatacagCTATGAGGATGAGCCTCCAGAACCTGAGATTGAG
EST: gi|211132182|gb|FL066419.1|FL066419
EST:     CGCGCGGGCGGA--SATGGCGGACGACGATTACAACGAAATCGACATGGG                         CTATGAGGATGAGCCTCCAGAACCTGAGATTGAG
genomic: CGCGCGGGCGGAGCCATGGCGGACGACGATTACAACGAAATCGACATGGGgttcgactct ... tgttatacagCTATGAGGATGAGCCTCCAGAACCTGAGATTGAG
EST: gi|211133098|gb|FL066420.1|FL066420
EST:     CGCGCGGGCGGAGCCATGGCGGACGACGATTACAACGAAATCGACATGGG                         CTATGAGGATGAGCCTCCAGAACCTGAGATTGAG
genomic: CGCGCGGGCGGAGCCATGGCGGACGACGATTACAACGAAATCGACATGGGgttcgactct ... tgttatacagCTATGAGGATGAGCCTCCAGAACCTGAGATTGAG
EST: gi|211131249|gb|FL066401.1|FL066401
EST:     CGCGCGGGCGGAGCCATGGCGGACGACGATTACAACGAAATCGACATGGG                         CTATGAGGATGAGCCTCCAGAACCTGAGATTGAG
genomic: CGCGCGGGCGGAGCCATGGCGGACGACGATTACAACGAAATCGACATGGGgttcgactct ... tgttatacagCTATGAGGATGAGCCTCCAGAACCTGAGATTGAG
EST: gi|211133102|gb|FL066424.1|FL066424
EST:     TGGC-GACGACGATTACAACGAAATCGACATGGG                         CTATGAGGATGAGCCTCCAGAACCTGAGATTGAG
genomic: TGGCGGACGACGATTACAACGAAATCGACATGGGgttcgactct ... tgttatacagCTATGAGGATGAGCCTCCAGAACCTGAGATTGAG

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 10

GCAGCCGCAAGCCAAAACCCTAGCAAGCAAACCACCGGAGCAGCGGCGCTCGCGCGGGCGGAGCCATGGCGGACGACGATTACAACGAAATCGACATGGGgttcgactct ... tgttatacagCTATGAGGATGAGCCTCCAGAACCTGAGATTGAG




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