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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGATAAAAAATAGGACCCATGCTATCTACCACTGGAATCGCAATGATGATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccctccaccttttgcttgggcattgctttcaagtagcagggagaaatatgccatatcttgctgttgtgatgaactataagattgaaagttatc...

Basic information

species Glycine max
transcript GLYMA17G11790.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11790.1 (Glycine max), 5'ss of exon 9
lower sequence: AC211394.4_FGT004 (Zea mays), 5'ss of exon 9
TGGAGATAAAAAATAGGACCCATGCTATCTACCACTGGAATCGCAATGATGATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccctccaccttttgcttgggcattgctttcaagtagcagggagaaatatgccatatcttgctgttgtgatgaacta-taagattgaaagttatc-
|  || | ||||| |||||||||||||||||||| |||||| | || |||||||| ||    || ||  | ||| |  |  |  | ||||| || || ||||  ||  |||  || ||  | ||      | |   |||| |        | || |        |  | ||     |  | || ||||  ||  | | |   
TACAGCTGAAAAACAGGACCCATGCTATCTACCAGTGGAATAGAAACGATGATGGGAATCCTGTTCCAGCAGACACCGTAATGTTCCATAACCAATATTGgtgagtgtcct--actttgcggtttttatctacgggcaagcattgctttcagatgtaatccgcatgccagtctgactatattactaagggtggtaatgagac

upper sequence: GLYMA17G11790.1 (Glycine max), 5'ss of exon 9
lower sequence: AT5G34850.1 (Arabidopsis thaliana), 5'ss of exon 8
TGGAGATAAAAAATAGGACCCATGCTATCTACCACTGGAATCGCAATGATGATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccctccaccttttgcttgggcattgctttcaagtagcagggagaaatatgccatatcttgctgttgtgatgaactataagattgaaagttatc
|||| ||||| ||  | || || ||||| ||||||||||| |||||||||||||| ||||||||  | || ||    |||||| | || || ||||||||||| |||   || |  | |  | |  | | |  |    |||| | |    | | |||   ||    |    |   |||  |                   
TGGATATAAAGAACCGAACACACGCTATATACCACTGGAACCGCAATGATGATGGGAAGAAAGTGGCAACGGATGAATTTGTATTACACAACCAGTACTGgtaagtt--ttctatttctcacgttagtaatctt----agtaactgc---atagatggagtactaagtgaatacaatgcgcag-----------------

upper sequence: GLYMA17G11790.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv04s0008g06520.t01 (Vitis vinifera), 5'ss of exon 9
TGGAGATAAAAAATAGGACCCATGCTATCTACCACTGGAATCGCAATGATGATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccctccaccttttgcttgggcattgctttcaagtagcagggagaaatatgccatatcttgctgttgtgatgaac-tataagattgaaagttatc
||||||| || ||||| ||||||||  ||||||| |||||||| ||||||||||| || |||||||| ||||| ||| | ||| |  | |||||||||||||| ||    |     | |   ||      |||     || | || |   | || |  | ||| |   | |       | | | |    ||  |  |  | 
TGGAGATCAAGAATAGAACCCATGCATTCTACCATTGGAATCGAAATGATGATGGGAAAAAAGTACCAACTGATTCTGTCGTATTCTACAATCAGTACTGgtaagtattgttattttctccttttctttctgccaagtagcatcatgccaacatttagcttatatctgtctcacacccatcatgtgttgttagatttggt-

upper sequence: GLYMA17G11790.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv11s0118g00240.t01 (Vitis vinifera), 5'ss of exon 9
TGGAGATAAAAAATAGGACCCATGCTATCTACCACTGGAATCGCAATGATGATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccctccaccttttgcttgggcattgctttcaagtagcagggagaaatatgccatatcttgctgttgtgatgaactataagattgaaa-gttatc---
|||| |||||||| ||||| |||||  |||||| |||||| || |||  |||||| ||  ||||  | |||||||| |||||| |||| |||||||||||||  ||||  |      ||   |||   ||  |||   | ||    |   | | |  | | ||     ||    ||    ||   ||   |  | | ||     
TGGAAATAAAAAACAGGACACATGCATTCTACCGCTGGAACCGGAATAGTGATGGGAAACAAGTTTCAACTGACTCATTTGTATTGCACAATCAGTACTGgtgagttctttttttgcttattttgcatatcactt---aatactgagccaagacac-cgagattgatgtgcctcgaaacccttcgagtcagtgacgatactgca

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|208227204|gb|GE023633.1|GE023633
EST:     CAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTATTG                         GGGACACAATCGCAGAAGAAGAAAACT
genomic: CAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACT
EST: gi|209714893|gb|BW682058.1|BW682058
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|31459027|gb|CD401055.1|CD401055
EST:     ATGGCAAGAAAGTACCGACTGACTCTTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: ATGGCAAGAAAGTACCGACTGACTC-TTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|208091965|gb|GD890556.1|GD890556
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|209728181|gb|BW651616.1|BW651616
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|208088275|gb|GD889443.1|GD889443
EST:     GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193354505|gb|FK319013.1|FK319013
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|7685096|gb|AW755744.1|AW755744
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193433196|gb|FK393902.1|FK393902
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193681333|gb|FK624469.1|FK624469
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193470834|gb|FK436901.1|FK436901
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGC
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGC
EST: gi|193392304|gb|FK360129.1|FK360129
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATT
EST: gi|254335242|gb|GR846739.1|GR846739
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193635119|gb|FK579812.1|FK579812
EST:     AAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: AAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|209701995|gb|BW670532.1|BW670532
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTGCTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|151399107|gb|EV268978.1|EV268978
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGGCAG                      
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACT----Ggtaggttccc ... atgcatg
EST: gi|208086133|gb|GD881911.1|GD881911
EST:     TGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: TGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|208316365|gb|GE114049.1|GE114049
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193429649|gb|FK394527.1|FK394527
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAA
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTT-A
EST: gi|208306843|gb|GE110074.1|GE110074
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|13311818|gb|BG405469.1|BG405469
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193538845|gb|FK496373.1|FK496373
EST:     AAGTACCGACTGACTCTTTTGTTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: AAGTACCGACTGACTCTTTTG-TACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|207756753|gb|GD728549.1|GD728549
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|208104148|gb|GD903579.1|GD903579
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAG
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAG
EST: gi|208087151|gb|GD887199.1|GD887199
EST:     TGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACNGAAG
genomic: TGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAG
EST: gi|208052796|gb|GD853913.1|GD853913
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAGTCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTTA
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTT-A
EST: gi|193359451|gb|FK325908.1|FK325908
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193361887|gb|FK327791.1|FK327791
EST:     TGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAA
genomic: TGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTT-A
EST: gi|193332504|gb|FK301622.1|FK301622
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193342189|gb|FK308465.1|FK308465
EST:     GATGGCAAGAAAGTATCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
EST: gi|193434040|gb|FK400164.1|FK400164
EST:     GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTAGAAGCATTTTCTATTGAAAGTTA
genomic: GATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACT-GAAGCATTTTCTATTGAAAGTTA
EST: gi|209706577|gb|BW667830.1|BW667830
EST:     CTGCATAATCAGTACTG                         GGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT
genomic: CTGCATAATCAGTACTGgtaggttccc ... atgcatgcagGGGACACAATCGCAGAAGAAGAAAACTGAAGCATTTTCTATTGAAAGTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGATAAAAAATAGGACCCATGCTATCTACCACTGGAATCGCAATGATGATGGCAAGAAAGTACCGACTGACTCTTTTGTACTGCATAATCAGTACTGgtaggttccctccaccttttgcttgggcattgctttcaagtagcagggagaaatatgccatatcttgctgttgtgatgaactataagattgaaagttatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA