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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggttcactagtcattatatttttatttcacctgttcatattgcgattgcaagcttggagtgccttagctttagatgtttgacatttgtcgccttctttgtttcatttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGCATAGCACCATTTTCAAACGATGTTGCTTTTAATATTATAGAGAAAGAGC

Basic information

species Zea mays
transcript GRMZM2G305007_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G305007_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g54790.1 (Oryza sativa), 3'ss of exon 3
gtgaggttcactagtcattatatttttatttcacctgttcatattgcgattgcaagcttggagtgccttagctttagatgtttgacatttgtcgccttctttgtttcatttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGCATAGCACCATTTTCAAACGATGTTGCTTTTAATATTATAGAGAAAGAGC
               ||| |||| |   || |   | |  | |   |  | || |   |   |   || |    | | ||   | |  | | | ||| ||  || ||||||| ||||||||||  |||||||||| |||||||| || || ||||||||||| ||||| ||||||||||||||||  || ||||||||||| |||||||| | |||||
-------------tgcataatatatcagttgctagtttagacaactcagtggctattctcttgctactaaatgattggtg---ggccatggacacctcct--gtctcatttgttgcagGATGTGATTCCACCTGCGTACCTTGACGAACTTTCACTACTTCAAGACCGTATAGCACCATTTTCAACTGAGGTTGCTTTTAACATTATAGAAACAGAGC
















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|211541628|gb|FL367733.1|FL367733
EST:     GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCG                         GATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGC
genomic: GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCGgtgaggttca ... tttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGC
EST: gi|148941497|gb|EC886426.2|EC886426
EST:     GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCG                         GATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGC
genomic: GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCGgtgaggttca ... tttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGC
EST: gi|149069689|gb|EE158073.2|EE158073
EST:     GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCG                         GATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGC
genomic: GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCGgtgaggttca ... tttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGC
EST: gi|211152953|gb|FL361223.1|FL361223
EST:     GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCG                         GATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGC
genomic: GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCGgtgaggttca ... tttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGC

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: 42 (upstream exon), 49 (downstream exon)
Score: 66

GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCGgtgaggttca ... tttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGCATAGCACCATTTTCAAACGATGTTGCTTTTAATATTATAGAGAAAGAGC


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 36

GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCGgtgaggttca ... tttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGCATAGCACCATTTTCAAACGATGTTGCTTTTAATATTATAGAGAAAGAGC


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 4

GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCGgtgaggttca ... tttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGCATAGCACCATTTTCAAACGATGTTGCTTTTAATATTATAGAGAAAGAGC


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 24

GCATTTGTGAAGATCGCACAAGCAGTTTCGTCACGGCCGgtgaggttca ... tttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGCATAGCACCATTTTCAAACGATGTTGCTTTTAATATTATAGAGAAAGAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccttagctttagatgtttgacatttgtcgccttctttgtttcatttgctgcagGATGTTGTTCCACCTGCATACCTTGATGAGCTCTCACTACTTCAGGACCGCATAGCACCATTTTCAAACGATGTTGCTTTTAATATTATAGAGAAAGAGC
                gtttgac  putative branch site (score: 24)
                               ccttctttgtttcatt  putative PPT
                                        tttcattt  TA-rich tract