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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGATAATAAAGCTATTGGCTCACATGGAGCTGTATTTCTTCAAAGGCAGCTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaatttttaaatcgagttgtatcacttttttatccatgtgtgatgctcagatccttatgtagttttactttatattgctttctctctaatccag

Basic information

species Zea mays
transcript GRMZM2G139533_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139533_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g11050.1 (Oryza sativa), 5'ss of exon 6
CAGATAATAAAGCTATTGGCTCACATGGAGCTGTATTTCTTCAAAGGCAGCTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaatttt---------taaatcgagttgtatcacttttttatccatgtgtgatgctcagatcctta-tgtagttttactttatattgctttctctctaatccag
||||||| || || |||||||| ||||||||||  |||||  ||  | | ||||     || ||| | || ||||||||||| || |||||||||||||||||| | |         | ||| ||| ||  |   |||| | |  || | |||||||||||| || |   || |  | | || | |   ||| | | | || |||
CAGATAACAAGGCAATTGGCTCTCATGGAGCTGAGTTTCTCAAACAGAAACTTGAGGTCTCTAAAGATATTTCTGTTCTAACACACTGTAATACTGGCAGgtaaatgtgtgaaactgtgaattgagatgacttgtttttctttgtatatatgatgctcagattctgaacataatggtgcattttctctttttgt-tatgatgcag
















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|32910772|gb|CF015584.1|CF015584
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|76017068|gb|DT944238.1|DT944238
EST:     AACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: AACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|211541114|gb|FL234981.1|FL234981
EST:     CTTGCAAAT-CAAAAAAGATATCTGTTCTAACCCATTGTA-TACTGGCAG                         TCTTTGCA-CTGCTGGTTATGGAACT
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTT-GCAACTGCTGGTTATGGAACT
EST: gi|78084278|gb|DV512671.1|DV512671
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|60359093|gb|DN226066.1|DN226066
EST:     GATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: GATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|78116800|gb|DV535187.1|DV535187
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|37398320|gb|CF636472.1|CF636472
EST:     CTTGC-AATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCTCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|74244684|gb|DT652598.1|DT652598
EST:     CTTGCAAATTCAAAAA-GATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|71435544|gb|DR816594.1|DR816594
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|211133451|gb|FL234996.1|FL234996
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTTGGGGTTATACGCGCTCTTC
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTT-GGGGTTATACGCGCTCTTC
EST: gi|78091338|gb|DV519712.1|DV519712
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|211133445|gb|FL234990.1|FL234990
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCTCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|76921923|gb|DV168769.1|DV168769
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|78180539|gb|DV551032.1|DV551032
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|76285911|gb|DV025479.1|DV025479
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|88749182|gb|DY533323.1|DY533323
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTACCCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|6964770|gb|AW433463.1|AW433463
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGG-TATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|88756113|gb|DY540254.1|DY540254
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGGTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|74242198|gb|DT650112.1|DT650112
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|60347352|gb|DN214325.1|DN214325
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|211133442|gb|FL234987.1|FL234987
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTACCCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGGTATGGAAACTGCCCTTGGGGTTATACGCTCTCT-C
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAA-CTGCCCTTGGGGTTATACGCGCTCTTC
EST: gi|71767215|gb|DR965152.1|DR965152
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATA
EST: gi|78180978|gb|DV551351.1|DV551351
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTA
EST: gi|74233420|gb|DT641334.1|DT641334
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|71756819|gb|DR954756.1|DR954756
EST:     CCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|211133447|gb|FL234992.1|FL234992
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCCTTGGGGTTATACGCTCTCTTC
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCC-TTGGGGTTATACGCGCTCTTC
EST: gi|32855368|gb|CD995049.1|CD995049
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|74233419|gb|DT641333.1|DT641333
EST:     -TGCAAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: TTGC-AAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|88756070|gb|DY540211.1|DY540211
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|71445095|gb|DR826145.1|DR826145
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|71427098|gb|DR808148.1|DR808148
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
EST: gi|32856195|gb|CD995876.1|CD995876
EST:     CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAG                         TCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA
genomic: CTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCA

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: 48 (upstream exon), 48 (downstream exon)
Score: 114

CAGATAATAAAGCTATTGGCTCACATGGAGCTGTATTTCTTCAAAGGCAGCTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCATTCGGGGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

CAGATAATAAAGCTATTGGCTCACATGGAGCTGTATTTCTTCAAAGGCAGCTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCATTCGGGGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 263

CAGATAATAAAGCTATTGGCTCACATGGAGCTGTATTTCTTCAAAGGCAGCTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCATTCGGGGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 107

CAGATAATAAAGCTATTGGCTCACATGGAGCTGTATTTCTTCAAAGGCAGCTTGCAAATTCAAAAAAGATATCTGTTCTAACCCATTGTAATACTGGCAGgtaattttta ... tctaatccagTCTTGCAACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCATTCGGGGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTT