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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtatttattgtgatacaatacacagtttaattttgatatccatgtaaagtattacactatcatcctcattaaaagattttaacttttaagttagtt...

Basic information

species Glycine max
transcript GLYMA05G30830.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30830.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 5'ss of exon 8
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtatttattgtgatacaatacacagtttaattttgatatccatgtaaagtattacactatcatcctcattaaaagattttaacttttaagttagtt
||||||| ||| ||||| |||| ||||| ||||| |||  |||||| ||||| ||  | |||||||||||||||||||| || |||||||| |||||||||| |||   | |  | |  |  | ||  | ||  ||    | | | |||      ||   || |  |  ||||     | || |   |||  ||      
GGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAAGAgtaagt---tgtaataaacctttgcatggattctttccatttttcttgttttcatttgatctgttgtaatcatctt--ggttatctgtttccag------

upper sequence: GLYMA05G30830.1 (Glycine max), 5'ss of exon 8
lower sequence: AT3G26440.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtatttattgtgatacaatacacagtttaattttgatatccatgtaaagtattacactatcatcctcattaaaagattttaacttttaagttagtt
||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||| || || ||||||||||| || || |||||| | ||  | |||||||||| |||| |     || | |  |  | | | ||||   || |    | | || | ||      ||  | | |||  |                       
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactc----tgcttcttttgataatataatca-gaaactgttatgaaatgtt-----ttctacattattgcag----------------------

upper sequence: GLYMA05G30830.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 5'ss of exon 7
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtatttattgtgataca-atacacagtttaattttgatatccatgtaaagtattacactatcatcctcattaaaagattttaacttttaagttagtt
||||||| ||| | ||  |||| || |||||||| |||| ||| || ||||| || ||||||||||| || || || ||||| || |||||||||||||||||||| | | ||    | |  |    || || ||  ||  || | ||||    | ||  |                                        
GGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAAGAgtgagtttctcttactcttctcacttccatttaaaaatttctaactatgtttgttgttgtag---------------------------------------

upper sequence: GLYMA05G30830.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G13000.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtatttattgtgatacaatacacagtttaattttgatatccatgtaaagtattacactatcatcctcattaaaagattttaacttttaagttagtt
||||||| ||  |||||||||||||||||||||||||||| ||||||||| | || || |||||||||||||| ||  ||||| | ||  ||| ||||||||| || ||  |  | || | | ||| |   |  |||  ||  ||     ||   |    |    |   | | ||   | || |  || ||  |      
GGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAAGAgtgcgtcttcttactcattcta-acaaaacgtt-tttaaatcgccgcacgaatcctagtccagaaaatgtgaatatgtgcttctctctcttctgcag---

upper sequence: GLYMA05G30830.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 4
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtatttattgtgatacaatacacagtttaattttgatatccatgtaaagtattacactatcatcctcattaaaagattttaacttttaagttagtt
||||||||||  | ||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || ||||| ||||||||||||||||||||||| ||      || | ||   | |  ||  || ||  ||   |||       ||| | |      |||||     |||  |               
GGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAAGAgtgagtgttg-----gacataa---atatcttttttatggcatttgtgtttcagtctacccaacttatgtcattttccaattccag--------------

upper sequence: GLYMA05G30830.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 5'ss of exon 8
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtatttattgtgatacaatacacagtttaattttgatatccatgtaaagtattacactatcatcctcattaaaagattttaacttttaagttagtt
||||||||||  ||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || ||||| ||||||||||||||||||||||| ||      || | ||   | |  ||  || ||  ||   |||       ||| | |      |||||     |||  |               
GGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAAGAgtgagtgttg-----gacataa---atatcttttttatggcatttgtgtttcagtctacccaacttatgtcattttccaattccag--------------

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|208299059|gb|GE100490.1|GE100490
EST:     ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGA                         ATACTTAAAACTGGTGAAGAAGCATGGGTTGGAGATTTCACAGCCTGGTTT
genomic: ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtattt ... tctatcacagATACTTAAAACTGGTGAAGAAGCATGGGTTGGAGATTTCACAGCCTGGTTT
EST: gi|208281624|gb|GE073772.1|GE073772
EST:     ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGA                         ATACTTAAAACTGGTGAAGAAGCATGGGTTGGAGATTTCACAGCCTGGTTT
genomic: ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtattt ... tctatcacagATACTTAAAACTGGTGAAGAAGCATGGGTTGGAGATTTCACAGCCTGGTTT
EST: gi|208133221|gb|GD932162.1|GD932162
EST:     ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTT-AATGCAGAAGA                         ATACTTAAAACTGGTGAAGAAGCATGGGTTGGAAATTTCACAGCCTGGTTT
genomic: ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtattt ... tctatcacagATACTTAAAACTGGTGAAGAAGCATGGGTTGGAGATTTCACAGCCTGGTTT
EST: gi|193438151|gb|FK402170.1|FK402170
EST:     ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTT-AATGCAGAAGA                         ATACTTAAAACTGGTGAAGAAGCATGGGTTGGAAATTTCACAGCCTGGTTT
genomic: ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtattt ... tctatcacagATACTTAAAACTGGTGAAGAAGCATGGGTTGGAGATTTCACAGCCTGGTTT
EST: gi|193304306|gb|FK270335.1|FK270335
EST:     ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAGGA                         ATACTTAAAACTGGTGAAGAAGCACGGGTTGGAGA
genomic: ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtattt ... tctatcacagATACTTAAAACTGGTGAAGAAGCATGGGTTGGAGA
EST: gi|208187995|gb|GD986809.1|GD986809
EST:     ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGA                         ATACTTAAAACTGGTGAAGAAGCATGGGTTGGAAATTTCACAGCCTGGTTT
genomic: ATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtattt ... tctatcacagATACTTAAAACTGGTGAAGAAGCATGGGTTGGAGATTTCACAGCCTGGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtatttattgtgatacaatacacagtttaattttgatatccatgtaaagtattacactatcatcctcattaaaagattttaacttttaagttagtt

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