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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgatcgatcgatctttcactatagatctccaccagtacaaaaatgaatgaacgtatgcatgcggccgtttacatatgacgaaggatgatggtactgttgatagctttatactgcaacgactaaaacacactactcgctgatcgatgctgatggtttgcttttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG

Basic information

species Zea mays
transcript GRMZM5G836250_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836250_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 9
gtgagtcgatcgatcgatctttcactatagatctccaccagtacaaaaatgaatgaacgtatgcatgcggccgtttacatatgacgaaggatgatggtactgttgatagctttatactgca-acgactaaaacacactactcgctgatcgatgctgatggtttgcttttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG-------------
               |||| ||   | | | |  | |    || ||   |   || |  |||  ||  |  | |||        |      || ||  | |  | | || ||   |  | |    |  |  ||  | ||       |  ||   |  || ||     | |||  ||||||||||||||| || |||||||| |||||||| || || || |||||||||||||| ||| |||||| |||||| ||||| |||||             
-------------gtgatcattttttttgggtgacaatgtatataacc-tagctgtagttattaataggagcttttttgaccctc------tgttgtgattcataaaagtttctaataggatgtaatcaccaccaattaacattgtagtgacagtattgcttcctgatgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGGTACACATTAAGC

upper sequence: GRMZM5G836250_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 7
gtgagtcgatcgatcgatctttcactatagatctccaccagtacaaaaatgaatgaacgtatgcatgcggccgtttacatatgacgaaggatgatggtactgttgatagctttatactgca-acgactaaaacacactactcgctgatcgatgctgatggtttgcttttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG
               |||| ||   | | | |  | |    || ||   |   || |  |||  ||  |  | |||        |      || ||  | |  | | || ||   |  | |    |  |  ||  | ||       |  ||   |  || ||     | |||  ||||||||||||||| || |||||||| |||||||| || || || |||||||||||||| ||| |||||| |||||| ||||| |||||
-------------gtgatcattttttttgggtgacaatgtatataacc-tagctgtagttattaataggagcttttttgaccctc------tgttgtgattcataaaagtttctaataggatgtaatcaccaccaattaacattgtagtgacagtattgcttcctgatgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG

upper sequence: GRMZM5G836250_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
gtgagtcgatcgatcgatctttcactatagatctccaccagtacaaaaatgaatgaacgtatgcatgcggccgtttacatatgacgaaggatgatggtactgttgatagctttatactgcaacgactaaaacacactactcgctgatcgatgctgatggtttgcttttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG
                                                                     ||  |||    |  | || | ||       || ||||  |   | |  | |      |  || |      |  || ||   |  | ||         | ||| |||| ||||| ||||| || ||||| || || || ||||| ||| | |||||||||||||||||  |||||| ||| |||||||| || ||
---------------------------------------------------------------------gctctttgttgagcatgatgtata-----tcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataata--caagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG

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|78105896|gb|DV524314.1|DV524314
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCCCCGTCCCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|76282214|gb|DV021782.1|DV021782
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|149085230|gb|EE174737.2|EE174737
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|89759141|gb|DY688054.1|DY688054
EST:     AAGTACCTCAAAGATGGCTCGCCCCCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|93284534|gb|EB676798.1|EB676798
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|83279121|gb|DV943129.1|DV943129
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|50324976|gb|CO520102.1|CO520102
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGGGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|71768088|gb|DR966025.1|DR966025
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|86471231|gb|DY237601.1|DY237601
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|50331044|gb|CO526170.1|CO526170
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|149085229|gb|EE174736.2|EE174736
EST:     AAGTACCCCAAAGATGGCTCGCCCCCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCCCCGTCCCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|148932776|gb|EE285437.2|EE285437
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|78113531|gb|DV531922.1|DV531922
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTCCCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|148929799|gb|EE285436.2|EE285436
EST:     AAGTACCCCAAAGATGGCTCGCCCCCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTCCCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|88752752|gb|DY536893.1|DY536893
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|71770842|gb|DR968779.1|DR968779
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|149088445|gb|EE177548.2|EE177548
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|86473014|gb|DY239384.1|DY239384
EST:     AAGTACCCCAAAGATGGCTCGCCCCCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|149064612|gb|EE286483.2|EE286483
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACTGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|71317307|gb|DR795338.1|DR795338
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|74244032|gb|DT651946.1|DT651946
EST:     A-GTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCCTGCTATACGGCGGGTGTGTTTTTGT
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGG-TGTGTTTTTGT
EST: gi|110201016|gb|EC882913.1|EC882913
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|94476278|gb|EB705236.1|EB705236
EST:     AAGTACCCCAAAGATGGCTCGCCCCCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCCCCGTACCTTGCTATACGGCGGTGTGTCTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|50332538|gb|CO527664.1|CO527664
EST:     AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA
EST: gi|149099889|gb|EE185942.2|EE185942
EST:     AAGTACCCCAAAGATGGCTCGCCCCCAAGATCTTTGAGATACATTGGAAG                         TATGGTTGCTGACGTGCCCCGTCCCTTGCTATACGGCGGTGTGTTTTTGTA
genomic: AAGTACCCCAAAGATGGCTCGCCACCAAGATCTTTGAGATACATTGGAAGgtgagtcgat ... ttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgactaaaacacactactcgctgatcgatgctgatggtttgcttttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG
                                      tttgctttt  CT-rich tract
                                      tttgcttttattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgatcgatcgatctttcactatagatctccaccagtacaaaaatgaatgaacgtatgcatgcggccgtttacatatgacgaaggatgatggtactgttgatagctttatactgcaacgactaaaacacactactcgctgatcgatgctgatggtttgcttttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC