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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgggctgcccggccccttcggttctccagtctcttccggagttcgctgccgcccccgagcattagtctaatcttgggttcgattccgggccactctgcctcacttcgtcctccctctcctccgccag

Basic information

species Zea mays
transcript GRMZM2G177912_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 2
TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgggctgcccggccccttcggttctccagtctcttccggagttcgctgccgcccccgagcattagtctaatcttgggttcgattccgggccactctgcctcacttcgtcctccctctcctccgccag
||||||||||| || |||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||        |   |    | ||||   || ||  ||||       | || |    |||||| |||  |      ||      |   ||||| | |    ||||                             
TTCAACGTCCCCGATCTCCGCGTCGGCACGCTCGACTCCCTCCTCGCCCTCAGCGACGATCTCGTCAAGgta------acccatctcttctcttc---tccccgatctc-------gatctcccttgccccccagctctcacgcgattcctatt---attcctgccgctgctgcag---------------------------

upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G05470.1 (Glycine max), 5'ss of exon 2
TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgggctgcccggccccttcggttctccagtctcttccggagttcgctgccgcccccgagcattagtctaatcttgggttcgattccgggccactctgcctcacttcgtcctccctctcctccgccag
|||||| ||||  |||||||| |||| ||||| ||||| |||||| | |||||||||||||||| ||||||   |             | | |||   | |     || |  |  | |    |  |  | | || |     | | ||||    ||  || |      | |  |                              
TTCAACATCCCCAACCTCCGCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatc------------ctcattccactttttttcctttctccaaatcacttatcttctctgatc-----tttcatctccaatttaatgcattattatttag------------------------------

upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G26220.1 (Glycine max), 5'ss of exon 2
TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgggctgcccggccccttcggttctccagtctcttc-cggagttcgctgccgcccccgagcattagtctaatcttgggttcgattccgg--gccactctgcctcacttcgtcctccctctc-ctccgccag--------------------------
|||||  ||||  | ||||| ||||| ||||| |||||||||||| | |||||||| || |||||||||||| ||        |     | |        | ||   | |||   | | ||  ||        ||  |||      |  |  ||||   ||  ||  || | |  ||||   ||  |  |   | ||  |  ||  |                          
TTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAGgtacgtacaattcccaatcacacgaaaaacattcaccgttttcgttgcgatccttgatattgtggaaaattgcggataaatgtggttatgttgtggctgcaattgcgccttgtttgtttattggtttcattttgcttgatctgtttgtgtgtgtgtgtgtgcag

upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 2
TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgggctgcccggccccttcggttctccagtctcttccggagttcgctgccgcccccgagcattagtctaatcttgggttcgattccgggccactctgcctcacttcgtcctccctctcctccgccag
|||||| | ||  ||||||||||||| ||||| ||||| |||||| | |||||||||||||||| ||||||   |        ||     ||  |   | | || | |  || |   ||      || | |    ||||  | || ||        | ||||   |     ||| | | |                       
TTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaat--------cctcattccgccaaat-tacacttttctctgatcttg-----cgtctctatccatttatttattc----acctgcttcc--tctgtaatgcattattag---------------------

upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G07260.1 (Glycine max), 5'ss of exon 2
TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgggctgcccggccccttcggttctcca-gtctcttccggagttcgctgccgcccccgagcattagtctaatcttgggtt-cgattccgggccact-ctgcctcacttcgtcctccctctcctccgccag---------------
|||||| ||||  | ||||||||||| ||||| |||||||||||| | |||||||| ||   |||||||||| ||      | ||   | |         | |  | || ||   |  | || | |||   | || | ||  | |  |      || |   |    |   || |    ||| |  |      || |  || |   |               
TTCAACATCCCCAATCTCCGCGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATACCGTCAAGgtacgt-caaattcccaatcacaccaaaacattcgcgactatttacggttgcggttccgttgc-gatccttgatattgtggaaaattacagataaatgtggctgcaatttcattatgcttgatctgttttctgtgtgtgtgtgttcgtgcag

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|211359331|gb|FL325567.1|FL325567
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|71327563|gb|DR800390.1|DR800390
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|9953349|gb|BE639932.1|BE639932
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|78120131|gb|DV538515.1|DV538515
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211542143|gb|FL390828.1|FL390828
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTT
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTT
EST: gi|211218538|gb|FL338330.1|FL338330
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGS-ATGAYCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAG-CAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211114226|gb|FL350275.1|FL350275
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGAWCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211267792|gb|FL344631.1|FL344631
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211217973|gb|FL307283.1|FL307283
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|71303539|gb|DR787880.1|DR787880
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|8367294|gb|BE050239.1|BE050239
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211362192|gb|FL333555.1|FL333555
EST:     GCGTCGGCACCCTCGACTCCCTCSTYGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|148969238|gb|EE019992.2|EE019992
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|149104624|gb|EE290073.2|EE290073
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211316704|gb|FL359227.1|FL359227
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTTGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|67016433|gb|CO445182.1|CO445182
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211105804|gb|FL320712.1|FL320712
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211283545|gb|FL347777.1|FL347777
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211064773|gb|FL350726.1|FL350726
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211460898|gb|FL364621.1|FL364621
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211078718|gb|FL360383.1|FL360383
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCAAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|76288290|gb|DV027858.1|DV027858
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211414492|gb|FL334083.1|FL334083
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211381249|gb|FL356117.1|FL356117
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211467481|gb|FL327941.1|FL327941
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgggctgcccggccccttcggttctccagtctcttccggagttcgctgccgcccccgagcattagtctaatcttgggttcgattccgggccactctgcctcacttcgtcctccctctcctccgccag

- - - - - - - - - - - - - - - - - - -  CTCCTC