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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattttgtatttaacaagcacttcttgcatatagttactgtggtcttattggaaccagacttgattgtttttccttgccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG

Basic information

species Zea mays
transcript GRMZM5G818887_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 6
gtaaattttgtatttaacaagcacttcttgcatatagttactgtggtcttattggaaccagacttgattgtttttccttgccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG
|||| |  | |    |  |      |||||  |  |||      | |       |||   || |   ||  ||||  |||   ||| |||||||||||||| ||| ||||||||||||||||||||| ||||||||||| || ||||| || |||
gtaagtcattttgccattagaagtgtcttgt-tgcagtcctgaagat-------gaagttgattcatttaatttta-ttgttgttgcagTCAAGAATGCCACTAAAGCCTGAACTTGTGTTTGAAGATATCAGCCAAGATCATGCACGGAAGACG

upper sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 3'ss of exon 6
gtaaattttgtatttaacaagcacttcttgcatatagttactgtggtcttattggaaccagacttgattgtttttccttgccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG
|||| |  | |       |      |||||  |  |||      | |    |||         || |||   |||  |||   ||| |||||||||||||||||| ||||||||||||||||||||| |||||| ||||||| || || || |||
gtaagtcattttgcccttagaagtgtcttgt-tgcagtcttgaagatgaagttga--------ttcatttaatttgattgttgttgcagTCAAGAATGCCATTAAAGCCTGAACTTGTGTTTGAAGATATCAGC-AAGACCATGCGCGGAAGACG
















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|211329322|gb|FL012784.1|FL012784
EST:     TGACAAGTACTACCAAACTCCACGTGTCTGGGCTA-CTGGATATGACGAG                         TCAAGAATGC-ATTAATGCCCTGA-CTTGTGTTTGAAGACTTC-GCCAAGA
genomic: TGACAAGTACTACCAAACTCCACGTGTCTGG-CTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCC-TGAACTTGTGTTTGAAGACATCAGCCAAGA
EST: gi|86470328|gb|DY236698.1|DY236698
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|148960724|gb|EE011368.2|EE011368
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|32804145|gb|CD956381.1|CD956381
EST:     ATGACAAGTACTACCAA-CTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTA
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTA
EST: gi|76013821|gb|DT940991.1|DT940991
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|211435031|gb|FL327502.1|FL327502
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|60342765|gb|DN209738.1|DN209738
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|78091451|gb|DV519825.1|DV519825
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|78091450|gb|DV519824.1|DV519824
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|67010369|gb|CO439118.1|CO439118
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTNGA-GACATCAGCCAAGA
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTT-GAAGACATCAGCCAAGA
EST: gi|149045355|gb|EE047779.2|EE047779
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATC
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|76013820|gb|DT940990.1|DT940990
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|71313247|gb|DR793147.1|DR793147
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|71313249|gb|DR793148.1|DR793148
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TNCA-GAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGA
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagT-CAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGA
EST: gi|76016276|gb|DT943446.1|DT943446
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|15100603|gb|BI396394.1|BI396394
EST:     TGGATATGCCGAG                         TCCAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: TGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|76016277|gb|DT943447.1|DT943447
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
EST: gi|78113031|gb|DV531425.1|DV531425
EST:     ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAG                         TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC
genomic: ATGACAAGTACTACCAAACTCCACGTGTCTGGCTAACTGGATATGACGAGgtaaattttg ... gccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttactgtggtcttattggaaccagacttgattgtttttccttgccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG
                           acttgat  putative branch site (score: 5)
                                 ttgtttttccttgcc  CT-rich tract
                                attgttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattttgtatttaacaagcacttcttgcatatagttactgtggtcttattggaaccagacttgattgtttttccttgccattgtagTCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA