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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgcttaaaaaattattgtttctgatgttgaaccgaaaatgtttgtttccagccaaaatttcaactgtattaaaatgtgaacttttattctgagaag

Basic information

species Glycine max
transcript GLYMA11G07530.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
TATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgcttaaaaaattattgtttctgatgttgaaccgaaaatgtttgtttccagccaaaatttcaactgtattaaaatgtgaacttttattctgagaag
| ||||||||||||| || || |||||||||||||||||||| || ||| | ||  ||||||| ||| |||| || |||||||| || || || ||||||||| |      | |   ||   ||| | || | || ||  |||||| |           ||||  |||      |||      |    || | | |||| |  
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaac------tgatggatg--tgtgtgtgttttttaaaagaaaatata----------caaaccttctctaacattgcttctt---tttctctcctgatag-

upper sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 5
lower sequence: AT2G18230.1 (Arabidopsis thaliana), 5'ss of exon 5
TATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgcttaaaaaattattgtttctgatgttgaaccgaaaatgtttgtttccagccaaaatttcaactgtattaaaatgtgaacttttattctgagaag
  |||| ||||||||  | || ||||| |||||||| ||||| |||||  |||| || ||||||||||||||||| ||||| || ||||| || ||||||||       ||      ||  ||   | | ||||| |  | ||  || | ||   ||| ||       ||| |  || | ||   || |  | | | |     
CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctctcgcctcatc-ttagctttcatgttcatacaaacttgat-gtaaacaggcagtgaaataacagacttgagata--aaatactgtgcag-----

upper sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 5'ss of exon 4
TATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgcttaaaaaattattgtttctgatgttgaaccgaaaatgtttgtttccagccaaaatttcaactgtattaaaat--gtgaacttttattct-gagaag
| |||||||||||||||| || || ||||| ||||||||||| |||||  ||||||| ||||||||||| ||||||||||| || ||| |||||||||||||||      || | | |  ||  |  |  |      |   |  |  | | |||         | || ||   ||| |||||   | || |     ||| | | ||
TGTTCTTTACTCATCAGTTGTTTATCCACATAACTATGGTTTCATCCCTCGAACCATCTGTGAAGACAGCGATCCTATGGATGTCCTGATTCTAATGCAGgtagtgtcatttgacataccatcttaccacaatcatgatacattacatcttttttatttttctaattaaatcttataaaaattcatcaattcgccctctcgtgtag

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|22928719|gb|BU545858.1|BU545858
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTNTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|254328447|gb|GR835412.1|GR835412
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|192310086|gb|FK000650.1|FK000650
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|10254828|gb|BE822594.1|BE822594
EST:     GNNNCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|31469770|gb|CD411798.1|CD411798
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|192333274|gb|FK026155.1|FK026155
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|58022382|gb|CX709123.1|CX709123
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|22930561|gb|BU547700.1|BU547700
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|192321262|gb|FK014352.1|FK014352
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|192325458|gb|FK018399.1|FK018399
EST:     ATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: ATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|58018488|gb|CX705230.1|CX705230
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCNTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|192316544|gb|FK009313.1|FK009313
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTTTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
EST: gi|193495770|gb|FK461108.1|FK461108
EST:     GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAG                         GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG
genomic: GAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgc ... ttctgagaagGAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgcttaaaaaattattgtttctgatgttgaaccgaaaatgtttgtttccagccaaaatttcaactgtattaaaatgtgaacttttattctgagaag

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