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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGTTGGCACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctcttctcattttctttgtggtcaaggtatagcagtgagcatggattttaaattgataattttacccttttactgcag

Basic information

species Glycine max
transcript GLYMA11G09150.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g41790.2 (Oryza sativa), 5'ss of exon 1
GATTGTTGGCACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctcttctc--------attttctttgtggtcaaggtatagcagtga--gcatggattttaaattgataattttacccttttactgcag-----
  |  |||||||||| || || || || |||||||||||||| || || |||||||| ||||| || ||||| || ||||| |||||||||||||||||||| |||   ||  |         || ||  ||| | |    || |   || ||  || ||  |  || |     || |      | | ||| ||      
TGTCATTGGCACTCTTCGAGGATTCGATCAGTTTATGAATTTGGTCGTGGACAACACAGTGGAGGTCAATGGAAACGAGAAGAATGACATAGGGATGGTGgtaagtaaactctttggaatgagatctttcttgggattcctgtttcatagggatggcctgtttggtacagctccaactcctaaatataactccaagagtt

upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g29740.1 (Oryza sativa), 5'ss of exon 3
GATTGTTGGCACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctcttc------tcattttctttgtggtcaaggtatagcagtga--gcatggattttaaattgataatt-----ttacccttttactgcag-------------------------
 |||||||| || |||||||| || || |||||||||||||| || || |||||||| || || || ||||| ||||| || | ||| || || |||||||| || | |||        ||| || |||  | ||  |        | | |  ||| |||  || | | |  | ||      ||  | || | |  |                          
AATTGTTGGTACGCTCCGTGGATTCGATCAGTTTATGAATTTGGTGGTGGACAACACGGTAGAGGTCAATGGAAATGACAAGACTGATATTGGAATGGTGgtaagccttctgtgaagaatcacttgcttatttgtttaaactctatacttattgcaaggagatttactagcaagttgcaatatatacattgattatatgctgatgcccctaaatcatttgcag

upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G11500.1 (Arabidopsis thaliana), 5'ss of exon 3
GATTGTTGGCACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctcttctcattttctttgtggtcaaggtatagcagtgagcatggattttaaattgataattttacccttttactgcag----
| ||||||| ||||||||||||||||| ||||| |||||| | ||||| || |||||||| ||||| |||||  |||| |||| |||||| |||||||||||  ||     ||    | |||   |   | |   |      |   |||   ||||   || |  ||| |||  |||| ||| |     
GGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgtacgtttctctccatctctctaactcacccacagaatcttcttgtcatttgttttgt-ttaaacattctacttttttcctggatgcag

upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G23930.1 (Arabidopsis thaliana), 5'ss of exon 3
GATTGTTGGCACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc---ttctcattttctttgtggtcaaggtatagcagtgagcatggattttaaattgataattttacccttttactgcag----
| ||  ||| ||||| ||||| ||||| ||||| |||||| | ||||| || |||||||| || ||||| || || || ||||  ||||| ||||||||||| ||||      ||||   |  |||||| || ||  |   || |           | |  | ||||  ||||||  |  |  ||       
GGTTACTGGAACTCTTCGTGGGTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAGGTGAACGGTAACGACAAAACCGACATCGGGATGGTGgtaagtctctcgattctgtgtccctttgtcgttaatcttctgctgc----------tcttgactgatg-ttttactttggttttgggagcag

upper sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0007g03130.t01 (Vitis vinifera), 5'ss of exon 3
GATTGTTGGCACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctcttctcattttctttg----tggtcaaggtatagcagtgagcat--ggattttaaattg--ataattttacccttttactgcag---------------------
| | ||||| ||||| ||||| ||||||||||| |||||  | || || ||||||||||||||||||||||| |||||||||| ||| ||||| ||||||||  ||    || |||| || |||     |  ||    |||   | | | |||  |||| | | | ||  || |  | | |||||| |    |                     
GGTGGTTGGAACTCTTCGTGGGTTTGACCAGTTCATGAACCTGGTGGTGGACAACACTGTGGAAGTGAATGGAAATGAGAAAACTGATATAGGCATGGTGgtaggttaatttttcatcttgttttatttttctcttaatattttatttaccatttggatatgatactgtaattagctcagccttttgcaattgatgtcacaattgtacctgcag

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|18730335|gb|BM525820.1|BM525820
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGATGCGCTTGAACC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACC
EST: gi|31561892|gb|CD487730.1|CD487730
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|254346216|gb|GR859829.1|GR859829
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|298176503|gb|HO026738.1|HO026738
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCTGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|151398942|gb|EV268813.1|EV268813
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|192327127|gb|FK015519.1|FK015519
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|31467429|gb|CD409457.1|CD409457
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|31306974|gb|CD392177.1|CD392177
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|151412914|gb|EV282726.1|EV282726
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|19452429|gb|BM953839.1|BM953839
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|33388212|gb|CA851419.1|CA851419
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|6667111|gb|AW278570.1|AW278570
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
EST: gi|193327961|gb|FK295550.1|FK295550
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCT
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCT
EST: gi|151410461|gb|EV280276.1|EV280276
EST:     ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTG                         GTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC
genomic: ACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctc ... tttactgcagGTAATCAGAGGAAATAGTGTGGTCACTGTTGAGGCGCTTGAACCCGTGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGTTGGCACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctcttctcattttctttgtggtcaaggtatagcagtgagcatggattttaaattgataattttacccttttactgcag

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