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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGCTCCAAACTATAGCCACGGATTTTCAACGCATTTCCAAGATTCACGACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagtactacccttttctattttcttcttttcttttcttttttccccaattttttttaattgtttttttgtttttctttgtttacttttttaag

Basic information

species Glycine max
transcript GLYMA14G24270.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G24270.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os06g43570.1 (Oryza sativa), 5'ss of exon 3
TTCAGCTCCAAACTATAGCCACGGATTTTCAACGCATTTCCAAGATTCACGACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagtactaccct-tttctattttcttcttttcttttcttttttccccaattttttttaattgtttttttgtttttctttgtttacttttttaag
| ||||| || ||  | || ||||| || ||  |  | | |||||| ||||||||||||| |||||  ||||| |||||||||||||| || || ||  |||  || |     ||   ||| |    || |||||    || |||  |     ||    |||    |  ||   ||||   |  ||      |      
TGCAGCTGCAGACCGTCGCGACGGACTTCCAGAGGGTGTTCAAGATCCACGACAAGCTCTACATCGGCCTCTCCGGCCTCGCCACCGACGCGCAGACGCTgtgagtcgccgcgccagatttgtcccctcctctttgtgcttttttggtttagcatccggtttgggagaattagggtttcggtcggtcggtggtgcag--

upper sequence: GLYMA14G24270.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 5'ss of exon 2
TTCAGCTCCAAACTATAGCCACGGATTTTCAACGCATTTCCAAGATTCACGACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagtactacccttttctattttcttcttttcttttcttttttccccaattttttttaattgtttttttg---tttttctttgt-ttacttttttaag-
| ||||| || ||  | ||||| || || ||  |  | | |||||| ||||||||||||| |||||  ||||| |||||||||||||| || || ||  |||  ||    |    || |   |||||  |||        | | ||       || ||  | |  |||||   |   ||||  | ||       | |||    
TGCAGCTGCAGACGGTCGCCACCGACTTCCAGAGGGTGTTCAAGATCCACGACAAGCTCTACATCGGCCTCTCCGGCCTCGCCACCGACGCCCAGACGCTgtgggtgtcccggaactctcggattttgctctagaaccggcgtattgagttgcttgttagttagggttttgggggggttttgatgtgcgccgtgtgtttgcag

upper sequence: GLYMA14G24270.2 (Glycine max), 5'ss of exon 1
lower sequence: AT1G21720.1 (Arabidopsis thaliana), 5'ss of exon 2
TTCAGCTCCAAACTATAGCCACGGATTTTCAACGCATTTCCAAGATTCACGACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgta---tgtagtactacccttttctattttcttcttttcttttcttttttccccaattttttttaattgtttttttgtttttctttgtttacttttttaag--------
||||||| || || || ||||| ||||| ||  | || |||||||| |||||     ||||||||| ||| ||||| ||||||||||||| ||||||| ||||   | | || | | | | |    ||||| | |||  || | |||        |  |    | |     ||||| ||  |||||||||  | |||| |         
TTCAGCTACAGACAATCGCCACTGATTTCCAGAGAATCTCCAAGATCCACGATCGTGTCTTCATCGGTCTTTCTGGTCTCGCCACCGATGTTCAAACACTgtaaactatcgtgcaagcttctaaatttttcatatttgtttgtttttacattttgaagtgaactgagaagattttttttcctctttgttttgtcttttgatgtttgaag

upper sequence: GLYMA14G24270.2 (Glycine max), 5'ss of exon 1
lower sequence: EFJ32896 (Selaginella moellendorffii), 5'ss of exon 2
TTCAGCTCCAAACTATAGCCACGGATTTTCAACGCATTTCCAAGATTCACGACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagtactacccttttctattttcttcttttcttttcttttttccccaattttttttaattgtttttttgtttttctttgtttacttttttaag
|  |  |||| || ||||| ||||||||||| ||||||| |||||| || ||||||||||   |||   |  | || || ||  |||| |  || ||  |||| ||  |  |||  |    | |||| | | ||  || |  ||    | |    ||| |                                      
TGAATTTCCAGACGATAGCTACGGATTTTCAGCGCATTTTCAAGATCCATGACAAGCTCTATGTCGGATTAGCAGGGCTTGCTTCCGACGTCCAGACTCTgtaagtt-tcttactttgaatttttttgtgcgttctttctgattcgctcgctgcctttgtag------------------------------------

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|192318541|gb|FK011365.1|FK011365
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|151405517|gb|EV275331.1|EV275331
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTTAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|6914510|gb|AW396040.1|AW396040
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|37995705|gb|CF807294.1|CF807294
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|10233865|gb|BE802753.1|BE802753
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|192331116|gb|FK020336.1|FK020336
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|19346754|gb|BM891634.1|BM891634
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|298182182|gb|HO026357.1|HO026357
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|298176982|gb|HO023343.1|HO023343
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|298191795|gb|HO035877.1|HO035877
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|151410578|gb|EV280393.1|EV280393
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|207769518|gb|GD742112.1|GD742112
EST:     CTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: CTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|298198899|gb|HO042262.1|HO042262
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|12774129|gb|BG239056.1|BG239056
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|193678148|gb|FK618398.1|FK618398
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAG
EST: gi|16347157|gb|BI972752.1|BI972752
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|23726885|gb|BU761446.1|BU761446
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|17519828|gb|BM188870.1|BM188870
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|26059647|gb|CA802561.1|CA802561
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|4395893|gb|AI494890.1|AI494890
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|298191024|gb|HO038503.1|HO038503
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|7926292|gb|AW832318.1|AW832318
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|16348147|gb|BI973742.1|BI973742
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
EST: gi|298177393|gb|HO027174.1|HO027174
EST:     GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATT                         GTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG
genomic: GACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagta ... cttttttaagGTATCAGCGTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGCTCCAAACTATAGCCACGGATTTTCAACGCATTTCCAAGATTCACGACAAGCTCTTCATCGCTCTCTCTGGCCTCGCCACCGATGCTCAAACATTgtatgtagtactacccttttctattttcttcttttcttttcttttttccccaattttttttaattgtttttttgtttttctttgtttacttttttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT