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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatgccttcgtgtcagacgggtattttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA

Basic information

species Zea mays
transcript GRMZM2G147882_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g09300.3 (Oryza sativa), 3'ss of exon 5
---------------gtcatgccttcgtgtcagacgggtattttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA
               ||||||| ||| || |   | | |||||||   | |||| ||||| |||| | |||||||||||||||| || | ||  ||||||| || ||| |||||||| |||| ||||  ||||| || |||||||| || || ||||| || ||||| ||||||||||||||||||||||| |||||
gtggacaaaaaacaggtcatgcattcttgccgttcag-tattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA

upper sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 5
gtcatgccttcgtgtcagacgggtattttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA
||||||| ||| || |   | | |||||||   | |||| ||||| |||| | |||||||||||||||| || | ||  ||||||| || ||| |||||||| |||| ||||  ||||| || |||||||| || || ||||| || ||||| ||||||||||||||||||||||| |||||
gtcatgcattcttgccgttcag-tattttattacacaagaaacataacgaattctgtcgtttgatgttccttttttcatcagGTAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCA
















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|32924156|gb|CF028968.1|CF028968
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32858736|gb|CD998417.1|CD998417
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|78117759|gb|DV536146.1|DV536146
EST:     GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGT--A-A-G-----G                         -T--G-T--CAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|93014970|gb|EB640490.1|EB640490
EST:     GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|32924110|gb|CF028922.1|CF028922
EST:     GTCAATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
EST: gi|50323931|gb|CO519057.1|CO519057
EST:     GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAG                         GTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG
genomic: GTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAG

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: 39 (upstream exon), 49 (downstream exon)
Score: 5

GCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 331

GCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 297

GCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 31

GCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACGCTAAGGCTCCTGCACTACGAAGGTGGACAAGAAACAGgtcatgcctt ... ctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaccccgcaaggaacatgacgagtcctgtcgtttgatgttctttctatcgccagGTAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCA
                               gtttgat  putative branch site (score: 31)
                                       ttctttctatcgcc  CT-rich tract
                                          tttctat  TA-rich tract