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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag

Basic information

species Glycine max
transcript GLYMA03G32800.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 4
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag
 |||||||| ||||| ||||||||||| ||||||||||| || ||||| ||||||||||||||  | || ||||||||||| || || || || ||||||||       |||| |  ||    ||||  ||||   |||  | | ||    | | |  |  | |  |   | |   || |  |   |                          
CATTGAAAGTCTTGACCCAGCTTTGCTTCGACCTGGTCGGATAGACAGAAAGATTGAATTTCCGTTACCAGATATTAAAACCAGGAGGCGGATCTTCCAGgtgc-----ttttctacaat---gtttcaagtt---ctgtcttattg--gaaacctgcttcgttcttatcaatagtttttgggtgcag-------------------------

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 5'ss of exon 3
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag
 || ||||| ||||||||||| ||||| || |||||||| || ||  ||||||| ||||||||||| || ||||||||||| ||  | ||||| |||||||||   |    ||     || |  ||||     |      | ||   | |     | ||| ||   |||   |   |   |||| |     |  |  | |             
CATCGAAAGTCTTGATCCAGCATTGCTACGCCCTGGTCGCATAGATCGGAAGATAGAATTTCCTCTGCCAGATATTAAAACTAGGCGGCGCATCTTCCAGgtaaatatccatt-----agtatcttttagaacttcagaatgcatgataac----tgataagca-gttcctttggttctcatgaatgttgtgaatcgtgcag-----------

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G056569_T01 (Zea mays), 5'ss of exon 3
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgta--ggcacattttgtgaaagcaa-gttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag
 |||||||| |||||||| |||||||| || || || || || ||| ||||||||||||| |||||||| ||||||||||| ||||||||||| ||||||||   |  |||| |   || || ||  ||| || | ||| || |     || ||| |||  | | |||||  |      || ||   |    ||                      
CATTGAAAGTCTTGATCCTGCTTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaacatctgtagacagtaatatttgcattatcaatgttc----gtaatacctttttgtccttataatgaa-ggttgtaaaccgtgcag----------------------

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 3
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtag-gcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag
 |||||||| ||||||||||| ||||| || || || || || ||| ||||||||||||||||||| || ||||||||||| ||| ||||||| |||||||||  |     | ||| || |  | | ||    || ||      | ||||    |||||||  |||  | | |||| |||||       |||||  || |||| || |      
CATTGAAAGTCTTGATCCAGCCTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTTCCTCTACCAGATATTAAAACTAGACGACGCATCTTCCAGgtactgtgacgtctgtaaatgataatatttgcattaac------aatgtt----cttaataccctt--tgttctta-ttata------gaaggttgtaaacttgtgcag-----

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 4
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag
 |||||||| ||||||||||| ||||| || || |||||||||||||| ||||||||||| ||| | |||||| | || || ||  | ||||| ||||||||      || |  |||||||   || | |||     |  || | |   | | | | || || |  | | |     || | |   | |   |                     
TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctatgtgatgaaagc---ttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcag---------------------

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 4
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag
||| || || ||||| |||||  |||| |||||||| || ||||| ||||| || || || |||||||| ||||| |||||||||||||| || |||||||||   | || |  |   |   || |  ||  |  |   |||    |  |  |  |  |    | |   |  |   || | |   |||||                       
AATCGAGAGTCTTGACCCAGCACTGCTTCGACCTGGACGGATTGATAGGAAAATCGAGTTCCCTCTCCCAGATATCAAAACAAGAAGACGTATCTTCCAGgta---atatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttg-tgggttctgtttataaaatag--------------------

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 5'ss of exon 4
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacattttgtgaaagc-aagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatg--actaaaaggtcttatacttctgaaatttag
 || || || ||||| || ||  | ||  |||| || || || |||||||| || ||||| ||||| || ||||| |||||||||||||| || ||||||||   ||||  | ||||     ||||||||  | |   |   | | | || ||     || || |   | |  ||||||  |||  | ||  ||                      
GATCGAGAGTCTTGACCCGGCACTTCTTAGACCAGGCCGGATCGACAGGAAAATCGAATTCCCTCTTCCAGATATCAAAACAAGAAGACGTATCTTCCAGgttc-cacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggttt--ttaattgcatgccattattag----------------------

upper sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 4
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcac---------attttgtgaaagcaagtttt----cagtttca-ctgcttcactgttatatcttaatatgcttattctacttaatta-tatgactaaa-aggtcttatacttctgaaatttag
|||||||||  | |||||||||||||| || ||||||||||| || |||||||||||||| ||||| ||||| ||||||||||||||||||||||||||||||              ||| ||  || ||||  ||      | ||||| | |  |   ||| | | || |||   |  |     ||| |||| ||| |||||  |  ||| ||   | | || |  ||
AATTGAAAGTTTGGATCCAGCTTTGCTTCGGCCTGGTCGAATAGATAGGAAGATTGAATTCCCTCTTCCTGACATTAAAACAAGAAGACGCATTTTCCAGgtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcag

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|192327496|gb|FK019623.1|FK019623
EST:     AGATTGAATTTCCTCTCTCTGATATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAG-ATGACATTAGCTGATGATGTCAA
genomic: AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacat ... tgaaatttagATACACACATCAAGGATGACATTAGCTGATGATGTCAA
EST: gi|16278560|gb|BI942968.1|BI942968
EST:     AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
genomic: AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacat ... tgaaatttagATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
EST: gi|254329470|gb|GR839033.1|GR839033
EST:     AGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
genomic: AGACGCATTTTCCAGgtaggcacat ... tgaaatttagATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
EST: gi|58014587|gb|CX701329.1|CX701329
EST:     AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
genomic: AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacat ... tgaaatttagATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
EST: gi|58019738|gb|CX706480.1|CX706480
EST:     AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
genomic: AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacat ... tgaaatttagATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
EST: gi|151412684|gb|EV282496.1|EV282496
EST:     AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
genomic: AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacat ... tgaaatttagATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
EST: gi|254329469|gb|GR839032.1|GR839032
EST:     AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAG                         ATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT
genomic: AGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacat ... tgaaatttagATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGAAAGCCTTGATCCAGCTTTGCTGCGACCTGGTCGAATTGACAGGAAGATTGAATTTCCTCTCCCTGATATTAAAACAAGAAGACGCATTTTCCAGgtaggcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG