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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAGGGATATGAAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaatttagatataaggaaagaaaaaaactgttctggatttcttttgaaggagtatttgttggaagttttaattttttggcgattttaaaatggg...

Basic information

species Glycine max
transcript GLYMA14G24270.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G24270.3 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G092975_T01 (Zea mays), 5'ss of exon 3
GTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAGGGATATGAAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaatttagatataaggaaag-aaaaaaactgttctggatttcttttgaaggagtatttgttggaagttttaattttttg-gcgattttaaaatggg--
|  | || ||| ||||||| ||||| |||||||| || |||||||| ||||| || ||||||||||||||  | |||||||| || ||||| ||||| |||| |   ||||| | |||              || |||   ||||      |  ||   |  | | | |  |||||||||||||  ||  |   | |    |  
GGTTGGTGTTCAGGCACAAGCTGTATCAGCTGCGGGAGGAGAGGGACATGAAGCCCGAGACCTTTGCCAGCCTTGTCTCTGCGCTCCTCTACGAGAAGAGgtgag--aattttgctatcgtacttttggtggaattgtgtaggatactggat--agaccttctgggtagttgttttaattttttatgccctgccagagcatgga

upper sequence: GLYMA14G24270.3 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G045371_T02 (Zea mays), 5'ss of exon 3
GTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAGGGATATGAAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaa------tgcaatttagatataaggaaagaaaaaaactgttctggatttcttttgaaggagtatttgttggaagttttaattttttggcg-attttaaaatggg
|  | || ||| ||||||| ||||| |||||||| || |||||||| ||||| || ||||||||||||||  | |||||||| || ||||| ||||| |||| |      ||| | |  | | |  ||  |       |   |||||| |     |     | ||| |||||     |||||| ||||    |   |   | |    
GGTTGGTCTTCAGGCACAAGCTGTATCAGCTGCGCGAGGAGAGGGACATGAAGCCTGAGACCTTTGCCAGCCTTGTCTCTGCGCTCCTCTACGAGAAGAGgtgaggattttgctagtgcgcttttgggggaattgtgtaggattctgggtaaacctactgcgggtagttgtta----ttttaaattttgaatgcgctgccagac---

upper sequence: GLYMA14G24270.3 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 5'ss of exon 3
GTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAGGGATATGAAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaatttagatataaggaaagaaaaaaactgttctggatttcttttgaaggagtatttgt--tggaagtttta---attttttggcgattttaaaatggg
| |||||||| |||||||||||||| ||||| || || |||||||||||||| || || |||||||| ||  | || |||||||| || ||||||||||||| |  |  ||     || |   |||        | |  |   ||| || ||   |    ||||   ||||  | |||   |   ||||  | ||||    |  |
GGCTTGTTTTTCGGCACAAACTGTATCAGCTTCGAGAGGAGAGGGATATGAAGCCCGAAACCTTTGCAAGCCTTGTATCTGCTCTTCTTTATGAGAAAAGgttactcgctt-----attactgaagtttttgtttatcatattttttttctgtttggaattttgaaatggacttattatgcaacatttgctggtttttctttttg

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|26047837|gb|CA784494.1|CA784494
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|10233865|gb|BE802753.1|BE802753
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTACGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|192331116|gb|FK020336.1|FK020336
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|26059647|gb|CA802561.1|CA802561
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|151405517|gb|EV275331.1|EV275331
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|19346754|gb|BM891634.1|BM891634
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|192318541|gb|FK011365.1|FK011365
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|37995705|gb|CF807294.1|CF807294
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|23726885|gb|BU761446.1|BU761446
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|9819697|gb|BE555210.1|BE555210
EST:     CTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: CTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|298182182|gb|HO026357.1|HO026357
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|298176982|gb|HO023343.1|HO023343
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|298191795|gb|HO035877.1|HO035877
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|6914510|gb|AW396040.1|AW396040
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|207769518|gb|GD742112.1|GD742112
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|298198899|gb|HO042262.1|HO042262
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|12774129|gb|BG239056.1|BG239056
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|17519828|gb|BM188870.1|BM188870
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTTTTCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|7233789|gb|AW569132.1|AW569132
EST:     AACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|16347157|gb|BI972752.1|BI972752
EST:     AACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCCTCTATGACAAAAG                         GTTTGGGCCATATTTTTGCCCGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGC-TCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|4395893|gb|AI494890.1|AI494890
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|7926292|gb|AW832318.1|AW832318
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|298191024|gb|HO038503.1|HO038503
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|7233908|gb|AW569250.1|AW569250
EST:     AACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|16348147|gb|BI973742.1|BI973742
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|151410578|gb|EV280393.1|EV280393
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
EST: gi|298177393|gb|HO027174.1|HO027174
EST:     AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAG                         GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA
genomic: AAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaat ... tgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTGTTTTCCGGCACAAACTGTACCAGCTGCGTGAAGAGAGGGATATGAAACCAGAGACCTTTGCCAGTTTAGTCTCTGCTCTGCTCTATGAGAAAAGgtaatgcaatttagatataaggaaagaaaaaaactgttctggatttcttttgaaggagtatttgttggaagttttaattttttggcgattttaaaatggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaaa