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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttgtatttaacaagcacttcttgcatatagttactgtggtcttattggaaccagacttgattgtttttccttgccattgtag

Basic information

species Zea mays
transcript GRMZM5G818887_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 6
GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttgtatttaacaagcacttcttgcatatagttactgtggtcttattggaaccagacttgattgtttttccttgccattgtag
 |||||||| || |||||||| |||||||||||||| || |||||||| ||||||| |  | |    |  |      |||||  |  |||      | |       |||   || |   ||  ||||  |||   ||| ||
ATATGACAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGAGgtaagtcattttgccattagaagtgtcttgt-tgcagtcctgaagat-------gaagttgattcatttaatttta-ttgttgttgcag

upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 5'ss of exon 6
GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaa---attttgtatttaacaagcacttcttgcatatagttactgtggtcttattggaaccagacttgattgtttttccttgccattgtag
 ||||| || || |||||||| |||||||||||||| || |||||||| |||||||   ||||||   |||  |    ||| |||||  |  | |   ||   ||  |  |   | | ||||||||| || |            
ATATGATAAATATTACCAAACCCCACGTGTCTGGCTTACCGGATATGATGAGgtaagtcattttgcccttagaagtgtcttgttgca-gtcttgaagatgaagttgattcattta-atttgattgttgttgcag----------

upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 6
lower sequence: EFJ14759 (Selaginella moellendorffii), 5'ss of exon 6
GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttgtatttaacaagcacttcttgcatatagttactgtggtcttattggaaccagacttgattgtttttccttgccattgtag
||||||| |||||| ||||  |||| | || ||||||||||||||||||||||||| ||  | ||||     |    | || |||| ||||  ||  | | |  ||  |  |   |  | |                    
GTATGACCAGTACTTCCAAGTTCCAAGAGTATGGCTAACTGGATATGACGAGgtaa-ttaagcattt---tcgtctgtgttacatacagtt--tgctgacatgctgacataactttgaactcacag---------------

upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 6
lower sequence: EFJ26505 (Selaginella moellendorffii), 5'ss of exon 6
GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttgtatttaacaagcacttcttgcatatagtt-actgtggtcttattggaaccagacttgattgtttttccttgccattgtag
||||||| |||||| ||||  |||| | || ||||||||||||||||||||||||| ||  | ||||     |    | || |||| ||||  |||   |    ||| |  || |                           
GTATGACCAGTACTTCCAAGTTCCAAGAGTATGGCTAACTGGATATGACGAGgtaa-ttaagcattt---tcgtctgtgttacatacagtttgctgacataaatttgaactcacag--------------------------

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|211435031|gb|FL327502.1|FL327502
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|86470328|gb|DY236698.1|DY236698
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|148960724|gb|EE011368.2|EE011368
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|32809166|gb|CD961400.1|CD961400
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCC
EST: gi|18179571|gb|BM380781.1|BM380781
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|211295447|gb|FL439736.1|FL439736
EST:     TGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: TGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|78113030|gb|DV531424.1|DV531424
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|32804145|gb|CD956381.1|CD956381
EST:     ATGACAAGTACTACCAA-CTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTA
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTA
EST: gi|71313247|gb|DR793147.1|DR793147
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|148971663|gb|EE022386.2|EE022386
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|50331764|gb|CO526890.1|CO526890
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|78091451|gb|DV519825.1|DV519825
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|149045355|gb|EE047779.2|EE047779
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATC
EST: gi|76013821|gb|DT940991.1|DT940991
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|60342765|gb|DN209738.1|DN209738
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|76013820|gb|DT940990.1|DT940990
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|71313249|gb|DR793148.1|DR793148
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TNCA-GAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGA
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagT-CAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGA
EST: gi|60341702|gb|DN208675.1|DN208675
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|78091450|gb|DV519824.1|DV519824
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|78022213|gb|DV490600.1|DV490600
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|211389689|gb|FL031640.1|FL031640
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|32826943|gb|CD966621.1|CD966621
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTA
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTA
EST: gi|110482572|gb|EE011367.1|EE011367
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|60393918|gb|DN226788.1|DN226788
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|37374451|gb|CF623583.1|CF623583
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|87156323|gb|DY401112.1|DY401112
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTG
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTG
EST: gi|78113031|gb|DV531425.1|DV531425
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|76016276|gb|DT943446.1|DT943446
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|76016277|gb|DT943447.1|DT943447
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|15100603|gb|BI396394.1|BI396394
EST:     TGGATATGCCGAG                         TCCAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: TGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC

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), 49 (downstream exon)
Score: 140

GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 331

GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 308

GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GTATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG