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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTGTGCCGTTTAGGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgactcccttacatagaagattaatgtttttaataattaggcacttgcatttactgttctttctttggtaaatag

Basic information

species Zea mays
transcript GRMZM2G020976_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g40030.2 (Oryza sativa), 5'ss of exon 3
AAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTGTGCCGTTTAGGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgactcccttacatagaagattaatgtttttaataattaggcacttgcatttactgttctttctttggtaaatag---------------------
|||||| || ||||| |||||||||||| |  ||||||| || ||||| ||  || ||||||| || ||||||||||| ||||||||||||||||| ||||||||||   | | | || || || |    | ||    | | |||| | | || |||   | |   ||   |  | | ||                      
AAATAGCGAGCCATCCGTGCCTTCTGATGCGTTATTCTTCGTTCCGTTCAGAATACTGTTGCGTACTACACCTCTTTCTTTGGCTTATTTACTCTATATGgtatgcttctttcttcacttataatacatttattaaatacacttagtcgcatgtattctatttgaattgaatcctgagtaatgttttccatcatggtaaaag
















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|71298002|gb|DR784970.1|DR784970
EST:     GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATG                         CTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
genomic: GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
EST: gi|31353270|gb|CD437627.1|CD437627
EST:     GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATG                         CTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
genomic: GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
EST: gi|71767957|gb|DR965894.1|DR965894
EST:     GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATG                         CTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
genomic: GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
EST: gi|71420101|gb|DR805011.1|DR805011
EST:     GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATG                         CTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
genomic: GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
EST: gi|93282589|gb|EB674853.1|EB674853
EST:     GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATG                         CTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
genomic: GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
EST: gi|78076866|gb|DV505300.1|DV505300
EST:     GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATG                         CTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
genomic: GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
EST: gi|31355902|gb|CD440259.1|CD440259
EST:     GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATG                         CTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
genomic: GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
EST: gi|148947455|gb|EC892886.2|EC892886
EST:     GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATG                         CTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT
genomic: GGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACT

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), 43 (downstream exon)
Score: 42

AAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTGTGCCGTTTAGGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACTCTACGACGCACAACAGTCGTGTTTACAATGACAATGGAGTATTTCCTGG


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 82

AAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTGTGCCGTTTAGGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACTCTACGACGCACAACAGTCGTGTTTACAATGACAATGGAGTATTTCCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

AAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTGTGCCGTTTAGGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACTCTACGACGCACAACAGTCGTGTTTACAATGACAATGGAGTATTTCCTGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 71

AAATAGTGATCCATCAGTGCCTTCTGATTCACTATTCTTTGTGCCGTTTAGGTTATTGTTGCGCACCACACCTCTTTCCTTGGCTTATTTACTCTACATGgtatgctgac ... tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACTCTACGACGCACAACAGTCGTGTTTACAATGACAATGGAGTATTTCCTGG