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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgacttctcacactctacaagtttgacttgatattgtataacctttagtaaatccatgtttaccaatacatgtccttttatttccag

Basic information

species Zea mays
transcript GRMZM2G037683_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037683_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 5'ss of exon 11
GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgact------tctcacactctacaagtttgacttgatattg-tataacctttagtaaatccatgtttaccaatacatgtccttttatttccag
|| |||||||| |||||||||||||| ||||| || ||||||||||||||||||||||||||| | |||      |||  |  |||      ||   || | |||| | ||  |  |     || | | ||  |  ||   ||    |  ||||||||
GTGTGGGATACGAAAACAACAGATTGTTTGCAAACATTCAAGCCACCACCTCCTTTGAGGgtaataactagcttgtctttccatctgatctcttctattaacattggtttaggccctcaatcatgcttcttaccttatg-gtggtgctccatttccag
















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|211475898|gb|FL358552.1|FL358552
EST:     CTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG                         GGAGGAGATGCATCTGTTAA
genomic: CTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgactt ... ttatttccagGGAGGAGATGCATCTGTTAA
EST: gi|67019283|gb|CO448032.1|CO448032
EST:     CTAAAACAACAGATTGCTTGCATACTTTCA-GCCACCACCTNCTTTGAGG                         GGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAA-TACTGAT
genomic: CTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgactt ... ttatttccagGGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGAT
EST: gi|211442071|gb|FL307771.1|FL307771
EST:     CTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG                         GGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGAT
genomic: CTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgactt ... ttatttccagGGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGAT
EST: gi|91873183|gb|EB403140.1|EB403140
EST:     TAAAACAACAGATTGCTTGCATACTTTTCA-GCCACCACCTCCTTTGAGG                         GGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGAT
genomic: TAAAACAACAGATTGCTTGCATACTTT-CAAGCCACCACCTCCTTTGAGGgtactgactt ... ttatttccagGGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGAT
EST: gi|211277652|gb|FL322062.1|FL322062
EST:     CTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG                         GGAGGAGATGCATCTGTTAATTCTG-CCATTTATTTC-AAAAAGTACTGAT
genomic: CTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgactt ... ttatttccagGGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGAT

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), 49 (downstream exon)
Score: 145

GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgactt ... ttatttccagGGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGATCACATTGTTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 65

GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgactt ... ttatttccagGGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGATCACATTGTTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgactt ... ttatttccagGGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGATCACATTGTTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 41

GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGGgtactgactt ... ttatttccagGGAGGAGATGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGATCACATTGTTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTAC