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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAAGTTATCACTTCCTCTGATAGATTTGAGATGTGGGGGGATGGATTGCAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttggctgatttgtggctaatagctaaatttttttgttctttctagtgtttttagtttaaatattgaaattctgaacttgcacttttaatgatt...

Basic information

species Glycine max
transcript GLYMA20G36740.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36740.2 (Glycine max), 5'ss of exon 5
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 5
GTAAAGTTATCACTTCCTCTGATAGATTTGAGATGTGGGGGGATGGATTGCAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttggctgatttgtggctaatagctaaatttttttgttctttctagtgtttttagtttaaatatt-gaaattctgaacttgcacttttaatgatt
| || | |   |||||| ||||||| |||||||||||||| |||||  | || || || || |||||||| || ||||| ||||||||||| || |||||||  |     | |   |  ||     | | | || || | ||||         ||  || | | | || || |  ||| |    ||  |            
GGAAGGCTCAGACTTCCACTGATAGGTTTGAGATGTGGGGAGATGGGCTTCAGACCCGTTCTTTTACCTTTATCGATGAGTGTGTTGAAGGTGTACTCAGgtgag-----ggtatctcctgat--gttgatgaagttgtatgtta-----gacgtaattggctgatattttcgtcatttttgttttatag-----------

upper sequence: GLYMA20G36740.2 (Glycine max), 5'ss of exon 5
lower sequence: EFJ09286 (Selaginella moellendorffii), 5'ss of exon 4
GTAAAGTTATCACTTCCTCTGATAGATTTGAGATGTGGGGGGATGGATTGCAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtct---tggctgatttgtggctaatagctaaatttttttgttctttctagtgtttttagtttaaatattgaaattctgaacttgcacttttaatgatt
| |||| | | |||||| ||||||  |||||||||||||| |||||   |||||||||||||||||| ||||| ||||||||||| || || ||  | |||| |||||   |  ||| ||| |||  ||| | |   |   |   ||||    | ||| ||| | ||     ||    |  || ||                 
GGAAAGCTCTAACTTCCACTGATAAGTTTGAGATGTGGGGTGATGGGAAGCAAACACGATCATTTACGTTCATCGATGAATGTGTGGAGGGTGTTTTGAGgtgtgtctctttttctgctttctgg--aattgatgg-tcgatcgattcta---aatgtcttttgctttttctttcttgtcgtgcacag---------------

upper sequence: GLYMA20G36740.2 (Glycine max), 5'ss of exon 5
lower sequence: EFJ12864 (Selaginella moellendorffii), 5'ss of exon 4
GTAAAGTTATCACTTCCTCTGATAGATTTGAGATGTGGGGGGATGGATTGCAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtct---tggctgatttgtggctaatagctaaatttttttgttctttctagtgtttttagtttaaatattgaaattctgaacttgcacttttaatgatt
| |||| | | |||||| ||||||  |||||||||||||| |||||   |||||||||||||||||| ||||| ||||||||||| || || ||  | |||| |||||   |  ||| ||| |||  ||| | |    |   | | |  |   | ||  ||| | ||     ||    |  || ||                 
GGAAAGCTCTAACTTCCACTGATAAGTTTGAGATGTGGGGTGATGGGAAGCAAACACGATCATTTACGTTCATCGATGAATGTGTGGAGGGTGTTTTGAGgtgtgtctctttttctgctttctgg--aattgatgg--tcgatcgatacta--aatgccttttgctttttctttcttgtcgtgcacag---------------

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|254317428|gb|GR826373.1|GR826373
EST:     AAACCACGATCATTTACCTTCA-TGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: AAA-CACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|31467396|gb|CD409424.1|CD409424
EST:     CATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCAATGAGAT
genomic: CATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|192309346|gb|FK000554.1|FK000554
EST:     CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|17964388|gb|BM271124.1|BM271124
EST:     CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|27445968|gb|CA953091.1|CA953091
EST:     GGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: GGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|58016749|gb|CX703491.1|CX703491
EST:     CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|27808934|gb|CB063356.1|CB063356
EST:     CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|58020306|gb|CX707048.1|CX707048
EST:     CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|193320018|gb|FK286869.1|FK286869
EST:     CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|13789918|gb|BG652509.1|BG652509
EST:     CAAACACGATCATTTACATTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|192302108|gb|FG995228.1|FG995228
EST:     CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|254317427|gb|GR826372.1|GR826372
EST:     CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|14008581|gb|BG725185.1|BG725185
EST:     CAAACACGATCATTTACATTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|209703623|gb|BW656579.1|BW656579
EST:     CAAACACGATCATTTACATTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|9260013|gb|BE348160.1|BE348160
EST:     ATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: ATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|9983774|gb|BE657882.1|BE657882
EST:     ATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAANNNGATTTCCGAGANNCAGTAAATATTGGAAGCGATGAGAT
genomic: ATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|6913727|gb|AW395257.1|AW395257
EST:     CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAG                         ATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGATTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAAGTTATCACTTCCTCTGATAGATTTGAGATGTGGGGGGATGGATTGCAAACACGATCATTTACCTTCATTGATGAATGTGTTGAAGGGGTGCTCAGgtatgtcttggctgatttgtggctaatagctaaatttttttgttctttctagtgtttttagtttaaatattgaaattctgaacttgcacttttaatgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG