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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttgattgttatgtggacgcaatatgtactcttaatatttttgaaatacctttctatttaagtttttatatctctaactactacagcatgtgatag

Basic information

species Zea mays
transcript GRMZM2G432128_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G432128_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 5'ss of exon 4
GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttgattgttatgtggacgcaatatgtactcttaatatttttgaaatacctttctatttaagtttttatatctctaactactacagca-tgtgatag
|||||| |||||||||||||||||||| ||||||||||||| |    ||  ||| |||| |    | |   ||  |     |    | |||  ||  |  ||    | |||| ||| |  ||| | || || | |   ||
GTACAATGTGGCTATTAAGTGTGCGACGATTACTCCAGgtaaaagatat-attaagtggcc----ttttatcttatgcagctaaaaagatatattcttcatttgactcttatctcttt--ctatttcaacactattccag
















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|148957374|gb|EC903424.2|EC903424
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211301308|gb|FL411053.1|FL411053
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211348619|gb|FL403648.1|FL403648
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211317120|gb|FL381346.1|FL381346
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211202503|gb|FL419113.1|FL419113
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGACAACACATGTGGAAGA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGA-AACACATGTGGAAGA
EST: gi|211332798|gb|FL423282.1|FL423282
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|149110655|gb|EE190535.2|EE190535
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211245761|gb|FL421854.1|FL421854
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211158137|gb|FL392765.1|FL392765
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|33101480|gb|CF061440.1|CF061440
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|31612230|gb|CD568852.1|CD568852
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|67031198|gb|CO459947.1|CO459947
EST:     GTACTACGCGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211531114|gb|FL426904.1|FL426904
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|149031177|gb|EE286335.2|EE286335
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211264490|gb|FL417909.1|FL417909
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211003472|gb|FL408513.1|FL408513
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|29130876|gb|CB381580.1|CB381580
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211097134|gb|FL375411.1|FL375411
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|31356012|gb|CD440369.1|CD440369
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|74237580|gb|DT645494.1|DT645494
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|148937601|gb|EC881791.2|EC881791
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|76286556|gb|DV026124.1|DV026124
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211516468|gb|FL412101.1|FL412101
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211414079|gb|FL428571.1|FL428571
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|32845300|gb|CD984981.1|CD984981
EST:     ACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: ACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211365953|gb|FL391119.1|FL391119
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGT
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGT
EST: gi|211113009|gb|FL402637.1|FL402637
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|148961311|gb|EE012038.2|EE012038
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|149055178|gb|EE156095.2|EE156095
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211392274|gb|FL373436.1|FL373436
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211500096|gb|FL423896.1|FL423896
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|50338700|gb|CO533826.1|CO533826
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|32844807|gb|CD984488.1|CD984488
EST:     ACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGAAGTTCATTTTGAACCACATGTGGAAGAGCCCAA
genomic: ACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211214727|gb|FL396531.1|FL396531
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|32844692|gb|CD984373.1|CD984373
EST:     ACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: ACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|18659665|gb|BM500459.1|BM500459
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|32940854|gb|CF045673.1|CF045673
EST:     ACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
genomic: ACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAA
EST: gi|211352901|gb|FL376492.1|FL376492
EST:     GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG                         ATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGT
genomic: GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGT

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: 270

GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 958

GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 1146

GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 1483

GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAGgtacatttga ... catgtgatagATGAAACTCGGGTTAAGGAGTTCAATCTGAAACACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG