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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacctcttcaattttccttctttggagcatgctcttgctgcttttgtcaacatagaataagtgcaagtactgattttggtttatccttccccctctccccctcag

Basic information

species Glycine max
transcript GLYMA09G32900.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G32900.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G386125_T01 (Zea mays), 5'ss of exon 9
GTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacctcttcaattttccttctttggagcatgctcttgctgcttttgtcaacatagaataagtgcaagtactgattttggtttatccttccccctctccccctcag
 | ||||| ||||  || || |||||||| |||||||||||||||||| |  ||||||||||  | || |||| |   ||||  ||   ||| ||| |||||| || |  | |  || |    |   |||   |      ||| || | ||   ||| | |  |   |      |||  |       |||    |  | |  |   |    
TTAGAGCGACTCTTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAATAACTGCCCCATTCTTGGTTGAAAAACAAGgtaattaagttttataaatgag-taaattgacaccgatgattgttgatctt---aaccttgctt---tctctacacttttggaaaactatgggacgacatggcatgc----

upper sequence: GLYMA09G32900.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G700662_T01 (Zea mays), 5'ss of exon 8
GTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacctcttcaattttccttctttggagcatgctcttgctgcttttgtcaacatagaataagtgcaagtactgattt-tggtttatccttccccctctccccctcag
 | ||||| ||||  || || |||||||| |||||||||||||||||| |  ||||||||||  | || |||| |   ||||  ||   | | ||| |||||| || |  |||  || |    |   |||   |      ||| || | ||  |         |     |   |    |  | |||     | |  |               
TTAGAGCGACTCTTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAATAATTGCCCCATTCTTGGTTCAAAAACAAGgtaattaagttctataactgag-taaattgacactgatgattgttgatcttaaccttgcttgctctacacttttggaaaactatgggacgacatggcatgc-----------

upper sequence: GLYMA09G32900.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G314386_T02 (Zea mays), 5'ss of exon 6
GTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacctcttcaattttccttctttggagcatgctcttgctgcttttgtcaacatagaataagtgcaagtactgattt-tggtttatccttccccctctccccctcag
 | ||||| |||   || || |||||||| |||||||||||||||||| |  ||||||||||  | || |||| |   ||||| ||   ||| ||| |||||| || |  |||  || |    |    |||  |      ||| || | ||  ||        |  |  | | |    |  | |||     | |  |               
TTAGAGCGACTCCTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAATAACTGTCCCATCCTTGGTTGAAAAACAAGgtaattaagttctataaatgag-taaagtggccctgatgattgttgatcttagcattgcttgctctgcactactggaaaactatgggacgacatgacatgc-----------

upper sequence: GLYMA09G32900.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G65960.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacctcttcaattttccttctttgga---gcatg--ctcttgc--tgcttttgtcaacatagaataagtgcaagtactgattttggtttatccttccccctctccccctcag-------------------------------------------------------------------
||||| ||||| |  ||||| ||||| ||||||||||||||||| ||| |  |||||||||| |||||||||||| ||||    || ||| |    ||||||   ||   ||||| | ||||||       |   | |||   || ||   ||   ||  |    |||| |   ||   |  | |    ||||  | ||    | |   ||   | ||                                                                   
GTTGAACGTCTATTTGGTGCTCTTTCGGCTCATATGTGGCCTGGGATGATTCTGAAATCTGGTGATAGGATAAATGAACCTGTGTTACCTCAAGGGGAAGgttaattgtttcttccactttcctctcccatatatgtatgagttcctgaaatgtcctttcccggttagagtttctgttcgaccaggaagtggtaga-ccgaaactcgacccagataagaaatcctggtgaggacatttcatttccacttggattcatgttgattgggtcttatatttcctctcag

upper sequence: GLYMA09G32900.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv07s0031g02260.t01 (Vitis vinifera), 5'ss of exon 5
GTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtatt-----ttacctcttcaattttccttctttggagcatgctcttgctgcttttgtcaacatagaataagtgcaagtactgattttggtttatccttccccctctccccctcag
|||||  |  ||   |||||||||||||||||||||||||||||||||    |||||||||| |||| |||||   |||||||||| ||||| ||  ||||| ||      || ||  ||    |  ||| |||      |  || |  | || || |     || | | || |     | ||||||    |  ||  | |               
GTTGATAGAATCCTGGGTGCACTTTCTGCTCATATGTGGCCTGGAATGACCCTGAAATCTGGTGATAAGATAATGGAACCATCATTGCCTGAAAACCAAGgttttagatgctatcttctctgcctgtcttttttttttttttttccttttactctt-tagctctacattcagcgagctaattgatttcatctggtctgttcag-------------

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|58025388|gb|CX712129.1|CX712129
EST:     -TGAAATTCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAG                         AGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG
genomic: TTGAAA-TCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacc ... tccccctcagAGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG
EST: gi|58015161|gb|CX701903.1|CX701903
EST:     ATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCNTGAGAAAGAAG                         AGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTTTTATCAG
genomic: ATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacc ... tccccctcagAGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG
EST: gi|51335725|gb|CO979591.1|CO979591
EST:     ATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAG                         AGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG
genomic: ATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacc ... tccccctcagAGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG
EST: gi|19269990|gb|BM886246.1|BM886246
EST:     ATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAG                         AGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG
genomic: ATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacc ... tccccctcagAGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG
EST: gi|13788706|gb|BG651297.1|BG651297
EST:     CTGAGAAAGAAG                         AGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG
genomic: CTGAGAAAGAAGgtattttacc ... tccccctcagAGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG
EST: gi|151395592|gb|EV265469.1|EV265469
EST:     ATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGA-G                         AGT-ATCT-CAGA-GA-TCTGAT-ATGA-CA-GAGTATGA-GTCT-ATCAG
genomic: ATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacc ... tccccctcagAGTTATCTTCAGAAGAATCTGATTATGAACAAGAGTATGAAGTCTTATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCGATAGGATAAATCAACCATCATTTCCTGAGAAAGAAGgtattttacctcttcaattttccttctttggagcatgctcttgctgcttttgtcaacatagaataagtgcaagtactgattttggtttatccttccccctctccccctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG