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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGCTATGATGTTGGATTCATTCCGCATAAAGATGTTGCTCTCCCTCAAGTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAGgtaaagttttttaagacatttgttgctccacttagttagattgtacgaaaaaattggtgcagattaggttttggggattggattttgctcaatgacttat...

Basic information

species Glycine max
transcript GLYMA01G02630.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G02630.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G38040.1 (Arabidopsis thaliana), 5'ss of exon 2
CCAGCTATGATGTTGGATTCATTCCGCATAAAGATGTTGCTCTCCCTCAAGTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAGgtaaagtt--ttttaagacatttgttgctccacttagttagattgtacgaaaaaattggtgcagattaggttttggggattggattttgctcaatgac-ttat--
| |||||  ||||||| |||||||| || |||||||||||| | |||||||| || |||||||||||||| |||||||| || |||||| | || ||  |||||| |   |  |    | ||| ||     |||  | |||||  |        |||| ||     |   | ||    ||    | ||      ||   |||   
CTAGCTACAATGTTGGTTTCATTCCTCACAAAGATGTTGCTTTGCCTCAAGTTCTTCAGCCATTTGCTCTCCCTGCTGGTGGAAATGATGTTGAGAATCGgtaaactaagtcctccctcttttattagga-actctggtagatcctggagttgtattgttg---gctcaatgttactaat--actgttaaatggtggtgttacag

upper sequence: GLYMA01G02630.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv03s0038g00680.t01 (Vitis vinifera), 5'ss of exon 2
CCAGCTATGATGTTGGATTCATTCCGCATAAAGATGTTGCTCTCCCTCAAGTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAGgtaaagttttttaagacatttgttgctccacttagttagattgtacgaaaaaattggtgcagattaggttttggggattggattttgctcaatgacttat-------
| || |||||||||||||| |||||||| || |||||||| |||||||||||  | |||||||||||||| ||  |||| || |  || ||| | ||||||| |     | |    |||||        | ||  ||  |||  | | ||   ||| | |||   |  |||    ||    |     |   |||| |||        
CAAGTTATGATGTTGGATTTATTCCGCACAAGGATGTTGCCCTCCCTCAAGTCTTGCAGCCATTTGCTCTCCCAACTGGAGGAAGGGACATAAAGAACAGgttaccaactct---gcattt--catctaagttttttgaatt-catggaattcttgattcagga-atttttcattgaccacagaagaccttatgaattactttgtga

upper sequence: GLYMA01G02630.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv00s0218g00090.t01 (Vitis vinifera), 5'ss of exon 3
CCAGCTATGATGTTGGATTCATTCCGCATAAAGATGTTGCTCTCCCTCAAGTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAGgtaaagttttttaagacatttgttgctccacttagttagattgtacgaaaaaattggtgcagattaggttttggggattggattttgctcaatgacttat---
| || ||||||||||||||||||||||| |||||||||||||||||||||||  | || || ||||||||||||||||| || |||||||||||||||||||||  | ||   |  | |||||| ||  | |||  || ||| |    |   | |  |  |   |  | |   |   |  ||  |    |  |  ||| |   
CAAGTTATGATGTTGGATTCATTCCGCACAAAGATGTTGCTCTCCCTCAAGTATTGCAACCTTTTGCTCTTCCTGCTGGAGGAAATGATATAGAAAACAGgtaacatcttc--aaccttttgttacttta-ttatatatattttttacatgtagttttagaatcttagctaaagaattgtgaggtgtaactctccctttttgg

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|16105262|gb|BI893002.1|BI893002
EST:     GTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAG                         AACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
genomic: GTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAGgtaaagtttt ... tgctttgcagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
EST: gi|9983448|gb|BE657556.1|BE657556
EST:     CTGGGGGGAATGATATAGAAAANAG                         NNNNACTCTTGGATTTTGGGNNGGTCATCGTAACTNNAAAATCAGAGTTAT
genomic: CTGGGGGGAATGATATAGAAAACAGgtaaagtttt ... tgctttgcagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
EST: gi|17963174|gb|BM269926.1|BM269926
EST:     GTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAG                         AACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
genomic: GTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAGgtaaagtttt ... tgctttgcagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
EST: gi|193658591|gb|FK604244.1|FK604244
EST:     CAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAG                         AACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
genomic: CAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAGgtaaagtttt ... tgctttgcagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
EST: gi|254319654|gb|GR830786.1|GR830786
EST:     TGCTACAGCCATTTGCTCTTCCTGCTNNNNNNNAATGATATAGAAAACAG                         AACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
genomic: TGCTACAGCCATTTGCTCTTCCTGCTGGGGGG-AATGATATAGAAAACAGgtaaagtttt ... tgctttgcagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
EST: gi|17963123|gb|BM269876.1|BM269876
EST:     GTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAG                         AACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT
genomic: GTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAGgtaaagtttt ... tgctttgcagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGCTATGATGTTGGATTCATTCCGCATAAAGATGTTGCTCTCCCTCAAGTGCTACAGCCATTTGCTCTTCCTGCTGGGGGGAATGATATAGAAAACAGgtaaagttttttaagacatttgttgctccacttagttagattgtacgaaaaaattggtgcagattaggttttggggattggattttgctcaatgacttat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgggg