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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGAGCACCTTACCTGCGCAAGGTGGACCTCACAATGTACAAAAGCTACAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttaccacaaaaaaccttcctacgtatcatattcccctctctttaaactacttgtttaccacaactatgtcactgaaaggataaccacgcatacac...

Basic information

species Glycine max
transcript GLYMA20G35270.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 2
GATGGAGCACCTTACCTGCGCAAGGTGGACCTCACAATGTACAAAAGCTACAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATG---Ggttagttacca--ca-aaaaaccttcctacgtatcatattcccctctctttaaactacttgtttaccacaactatgtcactgaaaggataaccacgcatacac-----------
   || ||||| |||||||||||||||||||| |  |||||||| |||||||| ||  | ||   |||  ||   || |||||| || ||||||||      ||| | |  |    ||    ||||| |  |   |   |||   |   |  ||||  |   ||   |     |    |  | |||    |  ||   ||||  ||           
---GGGGCACCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACAAGGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgctggccacgggaacctgcagaaacagattatcaactagtaattaatttgaatgcaaagtttgatc-cggaattgatgaaaacactgtgcatgaacctctctgtcag

upper sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 5'ss of exon 2
GATGGAGCACCTTACCTGCGCAAGGTGGACCTCACAATGTACAAAAGCTACAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgt--------tagttac-cacaaaaaaccttcctacgt-----atcatattcccctctctttaaactacttgtttaccacaactatgtcactgaaaggataaccacgcatacac
|| || || || ||||||||||||||||||||||  |||||||| ||||||   ||| | ||  | ||  | |  || |||||||||||||||||||| |||        || |||| || || | |  ||  ||  |     ||| ||||  | |   ||  |  || | |  |   | |  | | |  ||  ||  ||              
GACGGCGCGCCATACCTGCGCAAGGTGGACCTCAAGATGTACAAGAGCTACCTTGAGCTCTCCAAGGCACTCGAGAAGATGTTCAGCTCCTTCACCATTGgtaattatattaattacacataatatatgtttttatatataccatcgtattttcattcattccacatattcgcattttaaatgtctattcctttaaaaat--------------

upper sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G14550.1 (Arabidopsis thaliana), 5'ss of exon 2
GATGGAGCACCTTACCTGCGCAAGGTGGACCTCACAATGTACAAAAGCTACAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttaccacaaaaa-accttcctacgtatcat----attcccctctctttaaactacttgtttaccacaactatgtcactgaaaggata-accacgcatacac-------------------------------
|||||||| ||||| || || ||||| |||||||  |||||||  |||||||| ||  | |||||||||||||||||||||||||||||||| |||||||||  |      || | | |     | |  ||||||    |||    | | |    || | || ||      ||| ||     |      ||| || ||  ||  |                                
GATGGAGCTCCTTATCTTCGGAAGGTTGACCTCAAGATGTACACCAGCTACAAGGATCTCTCTGATGCCTTGGCCAAAATGTTCAGCTCCTTTACCATGGgtatgcattttcagacatataagtcgaattatcattattatttttgtgtttacttacaattttttctttttaacgatacagttttttccatatacgactaattaatatgataagttttgggattttgattaattaag

upper sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G23050.2 (Arabidopsis thaliana), 5'ss of exon 2
GATGGAGCACCTTACCTGCGCAAGGTGGACCTCACAATGTACAAAAGCTACAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttaccacaaa----aaaccttcctacgtatca----tattcccctctctttaaactacttgtttaccacaactatgtcactgaaaggataaccacgcatacac
|| || || || || ||| | || || |||||||  ||||||||||||||| | ||  | |||||||| ||||||||||||||||||||||| || ||||||  || |  | |||    ||| |       ||   |    |||   | | | || ||     |  ||||| |||  ||| |||   |||    |   ||        
GACGGTGCTCCATATCTGAGGAAAGTTGACCTCAAGATGTACAAAAGCTACCAGGATCTTTCTGATGCATTGGCCAAAATGTTCAGCTCCTTTACTATGGgtacgt-attagaaatttcaaatcggaaagtgtgaaaaaactatattcgtatattaaagtatatcatttactacatttat-tcatacaaaactcatgaacct------

upper sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 2
GATGGAGCACCTTACCTGCGCAAGGTGGACCTCACAATGTACAAAAGCTACAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttaccacaaaaaaccttcctacgtatca----tattcccctctctttaaactacttgtttaccacaactatgtcactgaaaggataaccacgcatacac
||||| || || || || |||||||||||| | |  |||||||| |||||| ||||  | |||||||| || | ||| |||||||| |||||||||||||||  || |    |  |      ||||| | | |    ||||   |  |  |||  |||    ||      | |||| | ||| |||  | | |  |   | || 
GATGGCGCGCCATATCTTCGCAAGGTGGACTTAAAGATGTACAAGAGCTACCAAGAACTCTCTGATGCATTAGGCAAGATGTTCAGTTCCTTCACCATGGgtatgt-attctatcagttgagcctacatgttacagttatttgacaattcttatgcta--aattctgtgaatctat-tgactcaaatcacatcatctgtttcaa

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|7924350|gb|AW830376.1|AW830376
EST:     CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGG                         GTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
genomic: CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttacc ... actggtgaagGTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
EST: gi|12774194|gb|BG239121.1|BG239121
EST:     GCCTTGGCCAAAATGTTCAGCTCCTTCACCATGG                         GTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
genomic: GCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttacc ... actggtgaagGTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
EST: gi|14990435|gb|BI316108.1|BI316108
EST:     CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGG                         GTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
genomic: CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttacc ... actggtgaagGTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
EST: gi|10235874|gb|BE804762.1|BE804762
EST:     CAAAGAGTTATCTGATGCCTTGGCCATAATGTTCAGCTCCTTCACCATGG                         GTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
genomic: CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttacc ... actggtgaagGTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
EST: gi|4260448|gb|AI416944.1|AI416944
EST:     CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGG                         GTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
genomic: CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttacc ... actggtgaagGTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
EST: gi|12774381|gb|BG239308.1|BG239308
EST:     CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGG                         GTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
genomic: CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttacc ... actggtgaagGTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
EST: gi|9820436|gb|BE555946.1|BE555946
EST:     CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGG                         GTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
genomic: CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttacc ... actggtgaagGTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
EST: gi|12689271|gb|BG155607.1|BG155607
EST:     CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGG                         GTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA
genomic: CAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttacc ... actggtgaagGTAACTATGGGGCCCAAGGAATGATAGACTTCATGAATGAGAGCAAGTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGAGCACCTTACCTGCGCAAGGTGGACCTCACAATGTACAAAAGCTACAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATGGgttagttaccacaaaaaaccttcctacgtatcatattcccctctctttaaactacttgtttaccacaactatgtcactgaaaggataaccacgcatacac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcccct