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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catagcacacctgttctgtttgacaattgtgtctttttttatgagtgcagcaactattgtacatttttggtccagttacttacgattaggatttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTTGCCTGAGATTTTCCCTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGC

Basic information

species Zea mays
transcript GRMZM2G412899_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412899_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 12
catagcacacctgttctgtttgacaattgtgtcttttt---ttat-gagtgcagcaactattgtacatttttggtccagttacttacgattagga----tttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTTGCCTGAGATTTTCCCTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGC
     | |     || |   |||||||| |   ||  |   | ||  ||| ||     ||| |||  | |     |||||| ||||   ||  |      |||| ||||||||||||| |||||||  |||||||||| || || ||||||||||||||||||||||||||||| || ||||| || || |||||||||||||| |||
----actctttaattgttcctgacaattatactttactggctcattaagtacaaatgttatggtaagtcta----ccagtttcttatagttgagtgcttctttttcagGTTTGTCTTGACATTTTCGTTAGGAGCAGGTCCAGTGCCAGGACTTCTTTTGCCTGAGATTTTCCCAAACAAAATACGGGCCAAGGCTATGGCTCTGTGC
















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|110961485|gb|EE181537.1|EE181537
EST:     CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT                         GTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
genomic: CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
EST: gi|78119069|gb|DV537453.1|DV537453
EST:     CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT                         GTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
genomic: CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
EST: gi|71321128|gb|DR797263.1|DR797263
EST:     CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT                         GTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
genomic: CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
EST: gi|78110186|gb|DV528601.1|DV528601
EST:     CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT                         GTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
genomic: CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
EST: gi|71759302|gb|DR957239.1|DR957239
EST:     CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT                         GTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
genomic: CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
EST: gi|148974491|gb|EE025274.2|EE025274
EST:     CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT                         GTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
genomic: CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
EST: gi|76015719|gb|DT942889.1|DT942889
EST:     CATGTGTATATCTTTCAGTTGGTGGCATTCTGTT                         GTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
genomic: CATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
EST: gi|50326105|gb|CO521231.1|CO521231
EST:     CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTT                         GTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT
genomic: CAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTT

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: 47 (upstream exon), 48 (downstream exon)
Score: 226

GCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTTGCCTGAGATTTTCCCTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 141

GCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTTGCCTGAGATTTTCCCTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTTGCCTGAGATTTTCCCTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 259

GCTTTTGCAATGGGGCTTCAGGCTGTTGGAGCAAACCGTCAGTATCTTGGTTCTGCATGTGTATATCTTTCAGTTGGTGGCATTCTGTTgtaagttcca ... atttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTTGCCTGAGATTTTCCCTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagcaactattgtacatttttggtccagttacttacgattaggatttttgcagGTTTGTCTTGTCATTTTCACTAGGAGCAGGCCCTGTCCCAGGACTTCTTTTGCCTGAGATTTTCCCTAATAAAATCCGAGCTAAGGCTATGGCTCTCTGC
                               tacttac  putative branch site (score: 259)
                                              tttttgc  putative PPT
         tattgtacattttt  TA-rich tract