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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttaggtcactccattgtgcaagtattcttaaacgcattgtttcctcattctttcttcacaccttaaccatttagatatatcttactctcacataaatcagcatatacctggcaatttctgctgttctctaattctttgtcacttctcttgtagGGTTGGAATAAGAA

Basic information

species Zea mays
transcript GRMZM2G484880_T04
intron # 2
splice site 3'
intron type U2

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|211058544|gb|FK994409.1|FK994409
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211061512|gb|FK994428.1|FK994428
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|76912438|gb|DV164732.1|DV164732
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|71434326|gb|DR815376.1|DR815376
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211058550|gb|FK994415.1|FK994415
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|6031476|gb|AW076378.1|AW076378
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211061507|gb|FK994423.1|FK994423
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211061514|gb|FK994430.1|FK994430
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211058549|gb|FK994414.1|FK994414
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211058545|gb|FK994410.1|FK994410
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|93284203|gb|EB676467.1|EB676467
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211058554|gb|FK994419.1|FK994419
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|13178287|gb|BG349545.1|BG349545
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211058547|gb|FK994412.1|FK994412
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|32913308|gb|CF018120.1|CF018120
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|26456042|gb|CA827625.1|CA827625
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211061508|gb|FK994424.1|FK994424
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211061515|gb|FK994431.1|FK994431
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|71438521|gb|DR819571.1|DR819571
EST:     TCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: TCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211058555|gb|FK994420.1|FK994420
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211061509|gb|FK994425.1|FK994425
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|71331879|gb|DR802817.1|DR802817
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|32865668|gb|CF005350.1|CF005350
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|31997934|gb|CD661839.1|CD661839
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA
EST: gi|211058548|gb|FK994413.1|FK994413
EST:     AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTC                         GGTTGGAATAAGAA
genomic: AAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA

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: 49 (upstream exon), 27 (downstream exon)
Score: 264

GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA


Block sizes: 44 (upstream exon), 14 (downstream exon)
Score: 112

GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 133

GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA


Block sizes: 48 (upstream exon), 14 (downstream exon)
Score: 136

GTTCAAAGGATCGAAAACCATGAAGATGAATGGCGCTACTTTGTCCATTATCTCgtaagtctta ... tctcttgtagGGTTGGAATAAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatatacctggcaatttctgctgttctctaattctttgtcacttctcttgtagGGTTGGAATAAGAA
                           ctctaat  putative branch site (score: 136)
                                 ttctttgtcacttctc  CT-rich tract
                              taattcttt  TA-rich tract