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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaacttaccggatagaagatccattttataactgcacgtgacatggaccatgatataaatatctgaattttctgctgcttctcaatgctaatacag

Basic information

species Zea mays
transcript GRMZM2G044092_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044092_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g67220.3 (Oryza sativa), 5'ss of exon 4
GAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaacttaccggatagaagatccatttt--ataactgcacgtgacatggaccatgatataaatatctgaattttctgctgcttctcaatgctaatacag------------------------------------------
||||||||||| |||||||| ||| | |||||  | || || |||||||||||||||||| | || ||||||||||||||| | | || | |  ||   || | ||  |   | || ||||| || |||| |     | ||| ||||    |  | ||  |  |  ||| |  |  | |||                                          
GAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTGgtatgttgagctaatcacatgagagcttcacatacaaaaattgcacatgccatgcatttccagatatatat---gacatcctttttttcatcagtaatgcttcagatcatctttctatgattgagactaattttatcatgcctgcag
















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|76282021|gb|DV021589.1|DV021589
EST:     AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG                         ACGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
genomic: AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
EST: gi|74243620|gb|DT651534.1|DT651534
EST:     AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG                         ATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
genomic: AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
EST: gi|148983451|gb|EE029465.2|EE029465
EST:     AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG                         ATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
genomic: AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
EST: gi|91874079|gb|EB404036.1|EB404036
EST:     AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG                         ATGGCTTGGGGGGAAATGTCAATGATCAA
genomic: AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAA
EST: gi|148945621|gb|EC890879.2|EC890879
EST:     AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG                         ATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
genomic: AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
EST: gi|149042713|gb|EE047228.2|EE047228
EST:     AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG                         ATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
genomic: AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
EST: gi|71312821|gb|DR792939.1|DR792939
EST:     AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG                         ATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
genomic: AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
EST: gi|71772492|gb|DR970424.1|DR970424
EST:     AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG                         ATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC
genomic: AGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACC

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: 38 (upstream exon), 47 (downstream exon)
Score: 56

GAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACCTCATCAATTTTATGATTTCGAAAG


Block sizes: 35 (upstream exon), 45 (downstream exon)
Score: 44

GAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACCTCATCAATTTTATGATTTCGAAAG


Block sizes: 35 (upstream exon), 47 (downstream exon)
Score: 69

GAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACCTCATCAATTTTATGATTTCGAAAG


Block sizes: 35 (upstream exon), 47 (downstream exon)
Score: 49

GAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTGgtatgctaaa ... gctaatacagATGGCTTGGGGGGAAATGTCAATGATCAAGGAGTCGCCTTCTATAATGACCTCATCAATTTTATGATTTCGAAAG