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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagtatatgctctttgccaactgatagatattgtagttaatggctgctactatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

Basic information

species Zea mays
transcript GRMZM2G362088_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
gtaagagtatatgctctt-tgccaactgatagatattgtagt-taatggc-tgctactatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
         |  | |||| ||  || |  |||  |   |||| | |     |||| | | ||  | |||||      ||||||||| || |  || |||| || || || || ||||||||||| |||||| ||||||| ||||| || || |||||||||||||||||||||||| | ||||||
--------gtcagatcttgtgtgaagttgtagtaaacatagtatcacaatatgctgcaaaattgttttgac------gatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG

upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
gtaagagtatatgctctttgccaactgatagatattgtagtta-atggctgctactatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAG----GACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
            |   |    || ||     |||| || || | ||       |  ||    | ||   ||||| | |||| | ||||  || || || |    |    ||||| |||||||||||   |||||||||||| ||||| || || |||||||| |||||||||||  |||||||||||
------------gtagtgcaaca-ctatgtaatatagttgtcatataaacaaaataatcatttttttctcatatag-tatgctttactgtttccatgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 6
gtaagagtatatgctctttgccaactgatagatattgtagttaatggctgctactatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAG----GACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
     |||  |  | || ||  |    |||| | |  ||  |||        | | | || | ||   |||||  ||||| | ||||  || || || |    |    ||||| |||||||||||  ||||||||||||| ||||| || || |||||||| |||||||||||  |||||||||||
---gtagtgca-acactctgtaat---atagttgtcata--taaacaaaataattgtttg-tttttctcatatatatatgctttactgtttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagagtatatgctctttgccaactga--tagatattgtagttaatggctgctactatatgatcttgaccatatgg-------atatggtgtacttgttg-cagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
|| ||  |   |   | |   || ||    |   ||  | | ||  | |   ||   || ||  ||||    |   |       | ||  |  | || ||  |||||||    |||    ||||||||||||   ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||||||||||
gtgagtttgcgtaaacgtcttcatctagattccgtagcgcattttgttgtcactttcat-tgtccttgcttcttcagtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG

upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
gtaagagtatatgctctttgccaactgatagatattgtagttaatggctgct-actatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
|| || ||  || || |||| |   |||  | |   |   ||  |   |  | || | |||  ||| | ||  ||  |||  | | |||   | ||||||     || || |||||||||||   |||||| || ||||| || || || |||||||||||||| |||||||| |||||||||
gtgagtgt-catactatttgtc---tgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtgtttattttattctt---gaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG

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|211392787|gb|FL282754.1|FL282754
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCACAAGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|60358607|gb|DN225580.1|DN225580
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCACAAGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|60341032|gb|DN208005.1|DN208005
EST:     TGGTTGGTAATAAGGCTGATTTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|37401257|gb|CF637991.1|CF637991
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCACAAGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGTCGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|60347047|gb|DN214020.1|DN214020
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|32854499|gb|CD994180.1|CD994180
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|50330000|gb|CO525126.1|CO525126
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|74243754|gb|DT651668.1|DT651668
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|149074254|gb|EE162627.2|EE162627
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|149078434|gb|EE167210.2|EE167210
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|74243753|gb|DT651667.1|DT651667
EST:     GGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|149094891|gb|EE180469.2|EE180469
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|211222474|gb|FL437630.1|FL437630
EST:     GTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: GTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|148970442|gb|EE021292.2|EE021292
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|148958503|gb|EC904742.2|EC904742
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|78091625|gb|DV519999.1|DV519999
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|78084796|gb|DV513189.1|DV513189
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|40336982|gb|CK371052.1|CK371052
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCACCAG-ACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTC
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGC-AGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTC
EST: gi|149094892|gb|EE180470.2|EE180470
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|32856098|gb|CD995779.1|CD995779
EST:     GTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: GTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|211392788|gb|FL282755.1|FL282755
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCACAAGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|18179553|gb|BM380763.1|BM380763
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|67021249|gb|CO449998.1|CO449998
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|78021899|gb|DV490286.1|DV490286
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|110201225|gb|EC883122.1|EC883122
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|60400505|gb|DN233312.1|DN233312
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCACAAGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|149014736|gb|EE044417.2|EE044417
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
EST: gi|13381875|gb|BG458550.1|BG458550
EST:     TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAG                         GATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG
genomic: TGGTTGGTAATAAGGCTGATCTACATGATAATCGAAGTGTATCCTCGCAGgtaagagtat ... cttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatggctgctactatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
                     tcttgac  putative branch site (score: 3)
           tactatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagtatatgctctttgccaactgatagatattgtagttaatggctgctactatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT