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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgatccttcctagtttcaatttcgatgccaggacatcttacacacttagtttgctgacttattttcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGATGAATGGATACCAATTAGGTGGTAAAAAGTTGAAAGTTCAACTCAAGAG

Basic information

species Zea mays
transcript GRMZM2G128809_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128809_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 8
gtaattgatccttcctagtttcaatttcgatgccaggacatcttacacacttagtttgctgacttattttcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGATGAATGGATACCAATTAGGTGGTAAAAAGTTGAAAGTTCAACTCAAGAG
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gtaattaacttgtcctaactgctaac-cattgattgtat---tatcatgctttgttaactggttcctgattgggtgcagGTTTTATAAGCTATGATTCTCCTGCTTCTGCACAGACAGCCATTAGTATGATGAACGGATACCAATTAGGTGGTAAAAAACTGAAAGTACAACTCAAGAG
















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|60354293|gb|DN221266.1|DN221266
EST:     GAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTG                         GTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGA
genomic: GAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTGgtaattgatc ... tcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGA
EST: gi|60400122|gb|DN232929.1|DN232929
EST:     GAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTG                         GTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGA
genomic: GAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTGgtaattgatc ... tcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGA
EST: gi|60356497|gb|DN223470.1|DN223470
EST:     GAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTG                         GTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGA
genomic: GAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTGgtaattgatc ... tcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGA
EST: gi|60344464|gb|DN211437.1|DN211437
EST:     GAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTG                         GTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGA
genomic: GAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTGgtaattgatc ... tcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGA

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

TTTGGTGACCATGATCTTGCAAATGCATTTCATAGTTTTGGTAGAGTACTGAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTGgtaattgatc ... tcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGATGAATGGATACCAATTAGGTGGTAAAAAGTTGAAAGTTCAACTCAAGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 25

TTTGGTGACCATGATCTTGCAAATGCATTTCATAGTTTTGGTAGAGTACTGAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTGgtaattgatc ... tcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGATGAATGGATACCAATTAGGTGGTAAAAAGTTGAAAGTTCAACTCAAGAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 53

TTTGGTGACCATGATCTTGCAAATGCATTTCATAGTTTTGGTAGAGTACTGAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTGgtaattgatc ... tcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGATGAATGGATACCAATTAGGTGGTAAAAAGTTGAAAGTTCAACTCAAGAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 31

TTTGGTGACCATGATCTTGCAAATGCATTTCATAGTTTTGGTAGAGTACTGAGTGCTAAAGTTTTTGTAGACAAGGCAACTGGTGTTAGTAAATGCTTTGgtaattgatc ... tcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGATGAATGGATACCAATTAGGTGGTAAAAAGTTGAAAGTTCAACTCAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgatgccaggacatcttacacacttagtttgctgacttattttcctggatagGTTTCGTAAGCTACGATTCTCCAGCTTCTGCACAAGCAGCCATTAGTGTGATGAATGGATACCAATTAGGTGGTAAAAAGTTGAAAGTTCAACTCAAGAG
                                tgctgac  putative branch site (score: 31)
                                      cttattttcct  CT-rich tract
                                     acttatttt  TA-rich tract