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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGCGTGTTGAGCAAAGTGTAAATAGGATGGTGACCATCATTGATCTTGCACGTAATATTCGTGAGCGGCATAACAAAGCTCTCAAAACACCACTCAAgtatgtctaggcttccttcaatttttgcatgtgtatgttttctgtgatgatgtgaatcactttggcagattgttcttataatatgttcttaaagcatgaa...

Basic information

species Zea mays
transcript GRMZM2G158627_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158627_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g43760.1 (Oryza sativa), 5'ss of exon 17
ATGAGCGTGTTGAGCAAAGTGTAAATAGGATGGTGACCATCATTGATCTTGCACGTAATATTCGTGAGCGGCATAACAAAGCTCTCAAAACACCACTCAAgtatgtctaggcttccttcaatttttgcatgtgtatgttttctgtgatgatgtgaatcactttggcagattgttcttataatatgttcttaaagcatgaa
||||||||||||||||||||||||| || ||| ||||||||||||||||||| || ||||||||||| ||||||||||||||  | ||||||||||| ||||||||  |   |  | | | || || | |    || |  |||      || |   | |         |   |||   |  |||  | |     ||||  
ATGAGCGTGTTGAGCAAAGTGTAAACAGAATGATGACCATCATTGATCTTGCCCGCAATATTCGTGAACGGCATAACAAAGCCTTGAAAACACCACTGAAgtatgttcatagtctcatgatttgtttcctaatgatttaatctagagatatttcgtttaggaaattgaaaatttcacgttgtataatatattgacatgtg
















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|71432888|gb|DR813938.1|DR813938
EST:     AACACCACTCAA                         GGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG
genomic: AACACCACTCAAgtatgtctag ... tgagtttcagGGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG
EST: gi|22715593|gb|BU197851.1|BU197851
EST:     GCACGTAATATTCGTGAGCGGCATAACAAAGCTCTCAAAACACCACTCAA                         GGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG
genomic: GCACGTAATATTCGTGAGCGGCATAACAAAGCTCTCAAAACACCACTCAAgtatgtctag ... tgagtttcagGGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG
EST: gi|74240586|gb|DT648500.1|DT648500
EST:     CTCTCAAAACACCACTCAA                         GGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG
genomic: CTCTCAAAACACCACTCAAgtatgtctag ... tgagtttcagGGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG
EST: gi|87156879|gb|DY401668.1|DY401668
EST:     GCACGTAATATTCGTGAGCGGCATAACAAAGCTCTCAAAACACCACTCAA                         GGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG
genomic: GCACGTAATATTCGTGAGCGGCATAACAAAGCTCTCAAAACACCACTCAAgtatgtctag ... tgagtttcagGGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG
EST: gi|26559569|gb|CA831804.1|CA831804
EST:     GCACGTAATATTCGTGAGCGGCATAACAAAGCTCTCAAAACACCACTCAA                         GGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG
genomic: GCACGTAATATTCGTGAGCGGCATAACAAAGCTCTCAAAACACCACTCAAgtatgtctag ... tgagtttcagGGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGG

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), 36 (downstream exon)
Score: 12

ATGAGCGTGTTGAGCAAAGTGTAAATAGGATGGTGACCATCATTGATCTTGCACGTAATATTCGTGAGCGGCATAACAAAGCTCTCAAAACACCACTCAAgtatgtctag ... tgagtttcagGGAGATGGTGGTTGTGCATCCAGACAATGACTTTCTTGAAGACATAACTGGTAAACTAAAAGAG




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