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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaatatccctccttgtccacctgcgattattgtccgtttgagttccgagagtgttctgctttctgactcggcgcccgccgcggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG

Basic information

species Zea mays
transcript GRMZM5G836250_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g64660.3 (Oryza sativa), 3'ss of exon 2
gtacgaatatccctccttgtccacctgcgattattgtccgtttgagttccgagagtgttctgc-tttctgactcggcgcccgccgcggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG
|||||||    |   ||| ||| | |   |  |||     | |  | || ||| ||  ||    ||| ||  |   | |  ||    | ||||||||||| ||||| |||||||||||||||||||| |||||||||||||||  ||||||||| | 
gtacgaactcactctcttctcccctta-aaccatt-----tctttgctcagagtgttctcaatatttatggtttttcact-gcgatcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCGCTGCGTGGGAA

upper sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 2
gtacgaatatccctccttgtccacctgcgattattgtccgtttgagttccgagagtgttctgc-tttctgactcggcgcccgccgcggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG--------------------------------------
|||||||    |   ||| ||| | |   |  |||     | |  | || ||| ||  ||    ||| ||  |   | |  ||    | ||||||||||| ||||| |||||||||||||||||||| |||||||||||||||  ||||||||| |                                       
gtacgaactcactctcttctcccctta-aaccatt-----tctttgctcagagtgttctcaatatttatggtttttcact-gcgatcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCGCTGCGTGGGAAGTGCGTAGCTTCGGATCAGAAACGCGACCTCTCTGCTT
















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|91877968|gb|EB407925.1|EB407925
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|149064613|gb|EE286484.2|EE286484
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|149085230|gb|EE174737.2|EE174737
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|149056940|gb|EE156494.2|EE156494
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|33466970|gb|CF244019.1|CF244019
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|78106830|gb|DV525248.1|DV525248
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGNCA-CGTTCGTGGACCCTAA
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAG-CAACGTTCGTGGACCCTAA
EST: gi|148938587|gb|EC882914.2|EC882914
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         C
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcag-
EST: gi|148938587|gb|EC882914.2|EC882914
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         C
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcag-
EST: gi|50327741|gb|CO522867.1|CO522867
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|89759142|gb|DY688055.1|DY688055
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|211007786|gb|FL012051.1|FL012051
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|149088446|gb|EE177549.2|EE177549
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|71314865|gb|DR794058.1|DR794058
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|149095912|gb|EE181574.2|EE181574
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|148983226|gb|EE029190.2|EE029190
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|71768089|gb|DR966026.1|DR966026
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|71770843|gb|DR968780.1|DR968780
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|148932776|gb|EE285437.2|EE285437
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|71317308|gb|DR795339.1|DR795339
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|211005021|gb|FL012048.1|FL012048
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|94476279|gb|EB705237.1|EB705237
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|91055488|gb|EB165906.1|EB165906
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|91877810|gb|EB407767.1|EB407767
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|149040104|gb|EE046754.2|EE046754
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|76282215|gb|DV021783.1|DV021783
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|74244032|gb|DT651946.1|DT651946
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|93284535|gb|EB676799.1|EB676799
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGATGAAGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|71438223|gb|DR819273.1|DR819273
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|78105897|gb|DV524315.1|DV524315
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
EST: gi|71757120|gb|DR955057.1|DR955057
EST:     TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC                         TGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG
genomic: TCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACCgtacgaatat ... cggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgagttccgagagtgttctgctttctgactcggcgcccgccgcggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG
                         ttctgac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaatatccctccttgtccacctgcgattattgtccgtttgagttccgagagtgttctgctttctgactcggcgcccgccgcggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG