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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGTACGTACTTTACGAGGGCGACACCGTTTCGGGGAACTTTGTTGTCGTCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaatctctatcacttttctcatctaatcatttgccctaatcacttgctaattgactcaattatcaatttactggtgagggtttatttttttag...

Basic information

species Glycine max
transcript GLYMA20G28900.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28900.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g53310.1 (Oryza sativa), 5'ss of exon 1
CGAGTACGTACTTTACGAGGGCGACACCGTTTCGGGGAACTTTGTTGTCGTCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaatctctatcacttttctcatctaatcatt-tgccctaatcacttgctaattgactcaattatcaatttactggtgagggtttatttttttag-------
||||| ||| |  |||||||| |||||||| ||||||||||| || ||||||||||| ||||| ||||||||||| || ||||||||||| ||  |||||||  |  |   | | |||    | ||| |||  || || |||  |      | | |    |  || || |  |  |   |  |  |||||| ||||||          
CGAGTTCGTGCCCTACGAGGGGGACACCGTGTCGGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCCGGCATCGACCTCACGgt--gcccgcccccgatc---ctcctcgtct--tcgttgtgcttttgattttcgatgcaaggatctataactagatgggtt-tatgggtttgttttttcgtgatctgg

upper sequence: GLYMA20G28900.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G009895_T01 (Zea mays), 5'ss of exon 1
CGAGTACGTACTTTACGAGGGCGACACCGTTTCGGGGAACTTTGTTGTCGTCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtg--caatctctatcacttttctcatctaatcatttgccctaatcacttgctaattgactcaattatcaatttactggtgagggtttatttttttag-
||||| ||| |  |||||||| |||||||| || |||||||| || || |||||||| ||||| ||||||||||| |||||||| ||||| ||  |||||||       | |||  |  | |        |  |||| |  ||  | |  | ||| |    |  ||      | |||   |  | | || || ||||  | | 
CGAGTTCGTTCCGTACGAGGGTGACACCGTGTCCGGGAACTTCGTCGTTGTCGACCACGACATCTTCTGGAGCTCCGATCACCCAGGCATCGACCTCACGgtacacacccgatccttgacccagccgcactacaatcctgcgcggttaa-atttgatgggagggtcgtggtacgattgggt--ttatgggttgttttgatggg

upper sequence: GLYMA20G28900.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G147046_T01 (Zea mays), 5'ss of exon 1
CGAGTACGTACTTTACGAGGGCGACACCGTTTCGGGGAACTTTGTTGTCGTCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaatctctatcacttttctcatc--taatc--atttgccctaatca--cttgctaattgactcaattatcaatttactggtgagggtttatttttttag
||||| ||| |  || |||||||||||||| || |||||||| || ||||||||||| ||||| ||||||||||| || ||||| || || ||  |||||||     ||| |  |  | |||| | || |  || ||  |||   |      |  || | |    |  ||   | || |||   |  | | ||||| ||||  |  
CGAGTTCGTGCCCTATGAGGGCGACACCGTGTCCGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgt--acacaaccgatccccctttccacagccgtagtccaattctgcgcggctaaactcgatcggaggatcgtgtttcgattgggt--ttatggtttgttttgat--

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|208203293|gb|GD996703.1|GD996703
EST:     TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
EST: gi|254323666|gb|GR840307.1|GR840307
EST:     TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
EST: gi|192309043|gb|FK001819.1|FK001819
EST:     TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
EST: gi|193416534|gb|FK384466.1|FK384466
EST:     CGTACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCTACAGTATCAAGGGAACCTCTGG
genomic: CG-ACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCC-ACAGTATCAAGGGAACCTCTGG
EST: gi|7041818|gb|AW471712.1|AW471712
EST:     TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
EST: gi|15337162|gb|BI497818.1|BI497818
EST:     ATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: ATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
EST: gi|8826075|gb|BE209867.1|BE209867
EST:     TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
EST: gi|7042157|gb|AW472051.1|AW472051
EST:     TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
EST: gi|151393248|gb|EV263123.1|EV263123
EST:     TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
EST: gi|13252173|gb|BG363076.1|BG363076
EST:     TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
EST: gi|298194416|gb|HO041064.1|HO041064
EST:     TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACG                         GTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT
genomic: TCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaa ... ttatctgcagGTGACAACTGCTGCAGGGAATACTGTCCACAGTATCAAGGGAACCTCTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGTACGTACTTTACGAGGGCGACACCGTTTCGGGGAACTTTGTTGTCGTCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaatctctatcacttttctcatctaatcatttgccctaatcacttgctaattgactcaattatcaatttactggtgagggtttatttttttag

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