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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatagttactcacggttacacttagtcatcaatttatttttacattctttgtgatagtgagttcttcatttctctctctcataagtcagtaagtcacaatgttactgctttttaattcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTT

Basic information

species Zea mays
transcript GRMZM2G178460_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178460_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g16040.1 (Oryza sativa), 3'ss of exon 4
gtcatagttactcacggttacacttagtcatcaatttatttttacattctttgtgat-agtgagttcttcatttctctctctcataagtcagtaagtcacaatgttactgctttttaattcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTT
                                    ||     | | ||||| | || ||| | ||    ||||     ||   | | |   | | |  | ||||  |||||||  | |||||||| |||||||||||||||| ||||||||| |||| |||||||||||||| ||||||||||| |||||||||||||||||||||
--------------------------------gtgataacgcca-actctttatcatcagtcaattacctattttggattcctgtcatt---tcaatttccatgtacctgctttgca-ttcagAAATTTTTCCGGAGAAAGGACGGAGAGCTTACTGTGTTTGGGAGACTTGCTGCTGGTGCTTGTGCGGGCATGACATCTACACTT

upper sequence: GRMZM2G178460_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G51870.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcatagttactcacggttacacttagtcatcaatttatttttacattctttgtgatagtgagttcttcatttctctctctcataagtcagtaagtcacaatgttactgcttttta-attcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTT
                 |||  |||  |  | | | | | || | | |    |   |  |   |     |  | ||| | |   || |  || | |    ||| | ||   ||||  ||||||||  | |||    | || ||||   |||| || ||| | || |||||||| ||||||||||| || ||||||||||||||  | 
-----------------ttagtcttttttgtta-tctgtattgaaactgacagcattcatcgttaaggaagatttctgtattgaaaat--gtgact---gatgcttctatattttgtattcagAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG
















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|71423587|gb|DR806089.1|DR806089
EST:     GCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAG                         AAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCC
genomic: GCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAGgtcatagtta ... tttaattcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCC




















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: 45 (upstream exon), 49 (downstream exon)
Score: 94

GTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAGgtcatagtta ... tttaattcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 55

GTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAGgtcatagtta ... tttaattcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

GTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAGgtcatagtta ... tttaattcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 111

GTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAGgtcatagtta ... tttaattcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttctctctctcataagtcagtaagtcacaatgttactgctttttaattcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTT
                                            ttttaat  putative branch site (score: 111)
                                       ctgcttttt  CT-rich tract
                                           tttttaattca  TA-rich tract