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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataattggttaacggcagtcccttttttttctttggttttatatatttgggttaagttacatagcacaaattgtgattgttcatttttaacgttattgtctgaaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTGTATGCTGATGGGATTACATCCTCAGATGGGGTAGCATCAACTGAATTCT

Basic information

species Zea mays
transcript GRMZM2G127739_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127739_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g40190.1 (Oryza sativa), 3'ss of exon 6
----------------------gtataattggttaacggcagt-----cccttttttttctttggttttat-----atatttgggt-taagttacatag---caca-aattgtgattgttcatt-tttaacgttattgtctgaaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTGTATGCTGATGGGATTACATCCTCAGATGGGGTAGCATCAACTGAATTCT
                      || | |    || ||  | ||     | || ||| | | |  |||| ||     ||    | || |||||      |   || | ||||   |||| ||||| |||||| || || | ||  |||  |||||||||||||| || ||||||||||||||||| || ||||||||||| || || ||||||||||| ||||||||||||||| ||||||| || || ||||
gtactattgttgttccattgttgtttgaacacttgacctcggttgatgcactgtttctacatctgtttcatgtcagatggcagtgtctaagtagtgctgagtcatataattacaattgctcattctttaacattgttatttgggatgatcagGCTGTTGATATTTCCCGAACGGAATATGAGCTCTCTGATATGGATATCCTTTACGCTGATGGGATAACATCCTCAGATGGGTTAGCATCTACAGATTTCT
















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|94473931|gb|EB702889.1|EB702889
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|71763610|gb|DR961547.1|DR961547
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|76017187|gb|DT944357.1|DT944357
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|78110170|gb|DV528585.1|DV528585
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|94475631|gb|EB704589.1|EB704589
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|71322062|gb|DR797719.1|DR797719
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|149070928|gb|EE159335.2|EE159335
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|78119468|gb|DV537852.1|DV537852
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|71308379|gb|DR790418.1|DR790418
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|71760704|gb|DR958641.1|DR958641
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|76014164|gb|DT941334.1|DT941334
EST:     GAAGTGAACTGCCATTCCCTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|71328662|gb|DR801008.1|DR801008
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|89252509|gb|DY624295.1|DY624295
EST:     TTCCCCCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: TTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|74241916|gb|DT649830.1|DT649830
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|71758063|gb|DR956000.1|DR956000
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|148979414|gb|EE026650.2|EE026650
EST:     AATG-GAACTGCCATTCTTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: AA-GTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|26457126|gb|CA828709.1|CA828709
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCAAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|21088970|gb|BQ401283.1|BQ401283
EST:     AGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: AGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|93283625|gb|EB675889.1|EB675889
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|74237568|gb|DT645482.1|DT645482
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|148929836|gb|EE285518.2|EE285518
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|149075131|gb|EE163624.2|EE163624
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|149100969|gb|EE187066.2|EE187066
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|149061146|gb|EE157406.2|EE157406
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|86469211|gb|DY235581.1|DY235581
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
EST: gi|149109394|gb|EE293282.2|EE293282
EST:     GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAG                         GCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG
genomic: GAAGTGAACTGCCATTCCTTCCACCTGCTGCCAGTTATTTTCTTGACAAGgtataattgg ... aaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatagcacaaattgtgattgttcatttttaacgttattgtctgaaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTGTATGCTGATGGGATTACATCCTCAGATGGGGTAGCATCAACTGAATTCT
                           ttttaac  putative branch site (score: 2)
                  attgttcatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataattggttaacggcagtcccttttttttctttggttttatatatttgggttaagttacatagcacaaattgtgattgttcatttttaacgttattgtctgaaatggccagGCTGTTGATATATCTCGAACGGAATATGAGCTGTCAGATATGGATATACTGTATGCTGATGGGATTACATCCTCAGATGGGGTAGCATCAACTGAATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG