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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctgattagtgaaatatagatattgcaatttggcctcaagtttaagctgcaaattgccgaattgattatcatcaaattctcattgaaatgtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG

Basic information

species Zea mays
transcript GRMZM2G118014_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118014_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 4
----gtctgatta-gtgaaatatagatattgcaatttggcctcaagtttaagctgcaaattgccgaattgattatcatcaaattc--tcattgaaatgtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG
    |||| || |  |||||   ||  | | |   ||||  |||      || |   | ||      || | || ||  | | |   || ||    |  ||    |||||||||||||| ||||||||||||||| ||| ||  |||||| ||||||||| | ||| ||||||| ||||| ||||||
gaaagtcttataatatgaaacggaggaagtac---ttggtttca----ctagttcgtagttataagttttactaccaaaatacttaatctttctcgtcaacatgtagATTTTGAAGGGAAAACTGATGATAAAATCAAGACCATGGAAGTGGTGGAAGAATTAAGATCTAAAAGGGCTGACATGCAG
















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|71445995|gb|DR827045.1|DR827045
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
EST: gi|211063251|gb|FL401238.1|FL401238
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAA-GGCCCCAG-AAGTAGTGGAA
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCC-AGGAAGTAGTGGAA
EST: gi|211384992|gb|FL172471.1|FL172471
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAA-GGCCCAGGAAGTAGT
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGT
EST: gi|76284913|gb|DV024481.1|DV024481
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
EST: gi|211400936|gb|FL417155.1|FL417155
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
EST: gi|149079348|gb|EE168324.2|EE168324
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
EST: gi|211517989|gb|FL372294.1|FL372294
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
EST: gi|211387614|gb|FL172477.1|FL172477
EST:     CAGCTGTCAAAACAGATCAAGGAAAAA-TGGTAGAAAGT-GATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAA-TAAAGCCCCAG-AAGTAGTGGAAG
genomic: CAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAA-GTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
EST: gi|211311591|gb|FL416726.1|FL416726
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
EST: gi|211440987|gb|FL029795.1|FL029795
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
EST: gi|76020071|gb|DT947241.1|DT947241
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
EST: gi|211019421|gb|FL374991.1|FL374991
EST:     GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTG                         ATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG
genomic: GCAGCTGTCAAAACAGATCAAGGAAAAAATGGTAGAAGTTGATGCCTTTGgtaattaccc ... gtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgcaaattgccgaattgattatcatcaaattctcattgaaatgtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG
               aattgat  putative branch site (score: 4)
                    attatcatcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgattagtgaaatatagatattgcaatttggcctcaagtttaagctgcaaattgccgaattgattatcatcaaattctcattgaaatgtactgacagATTTTGAAGGGAGAACTGATGATAAAATAAAGGCCCAGGAAGTAGTGGAAGAACTCAGAACTAAAAGAGCTGATATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - gctgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcaaa