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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgcatcttgcccttaagcattgctaccaacttgcgaatgaact...

Basic information

species Glycine max
transcript GLYMA13G26260.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G26260.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctac-----gtttctactc---ttaaagcgtgcgttttcttcttttagtgcttagttagactgcatcttgcccttaagcattgctaccaacttgcga-atgaact-------------
|  | || |||||||| || ||||||||   ||| |||||||| || ||||||||||| ||||||||||| || | |||||| || || ||||| ||| ||||   ||     |      |||   ||||| | |  |||   |   |||| | ||   |  || ||  | ||||  || |    |   ||  | |||    ||    |             
CGGTGGTGTTCTTCGACGTGACCATCGGGTCCATCCCCGCCGGCCGCATCAAGATGGAGCTCTTCGCCGACATCGTCCCCAAGACGGCGGAGAACTTCCGgtactgacccagagccctcgctcgccttaaaccctaggttccatctgtttaatcctgcttctga-tgtgt-ttgcttttgatggatctcactgatttgtttcatctgtttgtttggtttcag

upper sequence: GLYMA13G26260.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgta----tctacgttt----ctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgc------atcttgcccttaagcattgctaccaacttgcgaatgaact--------
|| | || |||||||| || ||||||||   |||  ||||||| || ||||||||||| ||||||||||| || |||||||| || || ||||| ||| |||      |||    |    |||  | |||| | |  ||||  ||  | |  | |||  ||   | ||      || |  | |||    |   ||   | | ||    |    |        
CCGTGGTGTTCTTCGACGTGACCATCGGGTCCATCGCCGCCGGCCGCATCAAGATGGAGCTCTTCGCCGACATCGCCCCCAAGACCGCGGAGAACTTCCGgtgatggcctaaaccttcaactaaccataaaccctaggtttcattggtattattctttcttctgccgctgatgtatttgacacttggatagatctctaatcgtgttgctttgtttgtttcag

upper sequence: GLYMA13G26260.1 (Glycine max), 5'ss of exon 1
lower sequence: AT2G38730.1 (Arabidopsis thaliana), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgta--tctacgtttctactcttaaagcgtgcgttttcttc--ttttagtgcttagttagactgcatcttgcccttaagcattgc----taccaacttgcgaatgaact----------------
                        | |||   || ||||||||||| ||||||||||| ||||||||||| ||||| |||||||| || || || |||||| |  |||    |  |   || |     |   || | ||   ||||| || ||| |      |  |||    |||      |||    ||     ||| |  |||| |                
------------------------TTGGTGGTATCCCCGCCGGTCGTATCAAGATGGAGCTCTTCGCCGACATTGCTCCCAAAACCGCTGAAAACTTCAGGCAGTTCTGTACTGGTGAACTCAGgtactcgattctgtttctttttaatgtttactccattcgattctctatcttcgttcctgcatcttattcgtttgaggttgaatttacgatttagtatttg

upper sequence: GLYMA13G26260.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv13s0084g00620.t01 (Vitis vinifera), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactctta-aagcgtgcgttttcttct---tttagtg-----cttagtt---agactgcatcttgcccttaagcattgctaccaacttgcgaatgaact------------
                        |||| | ||| ||||||||||| ||||||||||| |||||| |||| || ||||||||||| || || ||||||||| |  |  |      |   || | |  |   || | ||||   || | |      |||| ||    ||     || |   |||   | ||  |   |  |   ||||  | |            
------------------------TCGGCACCATCCCCGCCGGTCGCATCAAGATGGAGCTCTTCTCCGACATCGCCCCCAAAACCGCTGAAAATTTCAGGCAGTTCTGCACTGGCGAGTACAGgtttttattcttttctaacttcactcattttcttattttcaggatgatttccttttctttttctttcttcttatttgatgaatacaataatgatttgcag

upper sequence: GLYMA13G26260.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ31848 (Selaginella moellendorffii), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgcatcttgcccttaagcattgctaccaacttgcgaatgaact
|| |||||||||||||  |||| ||||| |     || || || || ||||||||||| ||||||||||| ||||  ||||| || |||||||| |||||||||      |||||||       ||||  | || |  ||       ||| ||   ||   | | ||                                 
CCGTCGTCTTCTTCGACATCACAATCGGGACGGCGCCTGCTGGGCGGATCAAGATGGAGCTCTTCGCCGACATTGTTCCCAAGACGGCCGAGAACTTCAGgtattag---ttctactt------cgtgtctgttttgtttcagagatttatttt--ctttctttggcag-------------------------------

upper sequence: GLYMA13G26260.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 1
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgcatcttgcccttaagcattgctaccaacttgcgaatgaact
|| |||||||||||||  |||| ||||| |     || || || || ||||||||||| ||||||||||| ||||  ||||| || |||||||| |||||||||      |||||||       ||||  | || || ||| || | ||  ||   ||   | | ||                                 
CCGTCGTCTTCTTCGACATCACAATCGGGACGGCGCCTGCTGGGCGGATCAAGATGGAGCTCTTCGCCGACATTGTTCCCAAGACGGCCGAGAACTTCAGgtattag---ttctactt------cgtgtctgtttttgtttcagagatttatttc-ctttctttggcag-------------------------------

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|58015177|gb|CX701919.1|CX701919
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|58025427|gb|CX712168.1|CX712168
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|298164520|gb|HO014165.1|HO014165
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|151408761|gb|EV278569.1|EV278569
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|298179325|gb|HO027796.1|HO027796
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|298174291|gb|HO017627.1|HO017627
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTAGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|58021016|gb|CX707758.1|CX707758
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|298170313|gb|HO018937.1|HO018937
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|31561148|gb|CD486986.1|CD486986
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|298180377|gb|HO025578.1|HO025578
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|208029483|gb|GD827899.1|GD827899
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|192333246|gb|FK026127.1|FK026127
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|16348066|gb|BI973661.1|BI973661
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|298172532|gb|HO019572.1|HO019572
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|151393429|gb|EV263304.1|EV263304
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|298183104|gb|HO028367.1|HO028367
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|163923182|gb|EH038294.1|EH038294
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAATACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|209704173|gb|BW664791.1|BW664791
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|58021929|gb|CX708670.1|CX708670
EST:     AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: AAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG
EST: gi|192298333|gb|FG992108.1|FG992108
EST:     GCCGATATTGCCCCCAAAACTGCCGAGAATTTCAG                         GCAGTTCTGCACTGGGGAGTACAG
genomic: GCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgt ... tatttggcagGCAGTTCTGCACTGGGGAATACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATCGTCTTCTTCGATGTCACCATCGGTAACATTCCCGCCGGTCGAATCAAGATGGAACTCTTCGCCGATATTGCCCCCAAAACTGCCGAGAATTTCAGgtatctacgtttctactcttaaagcgtgcgttttcttcttttagtgcttagttagactgcatcttgcccttaagcattgctaccaacttgcgaatgaact

- - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA