Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacttttattgaaacaatatttgtactctgatatgcatgtgttcttattatagtttaaatgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC

Basic information

species Glycine max
transcript GLYMA01G01460.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 1
----tgacttttattgaaacaatatttgtactctgatatgcatgtgttcttattatagtttaaatgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC
    | ||| || |||    ||  ||    ||  | | || |  || | |  || |   ||    || | ||     | ||  |      | ||     | ||| | |||||  |  | |||||  | ||  ||||||||||||| || || ||||| || ||||| |||||||| |||||||||||||| || || | ||| |
aaatttactcttgttgtttgaacctt---gcttaggtttgtaactgctgt-gttgtgccttctgcgtttttgcaattctaacagcggcatccattctcctacagACGGGTGACACCCTCATACAGCTCTACAACAATTTCATCACTGATTTCGAGACGAAGATCAATCTTCTCAAACTTGCGCATTTCGCGGTCATCGCTTCGC

upper sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 2
tgacttttattgaaacaatatttgtactctgatatg-catgtgttcttattatagtttaaatgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC
| |  |||    |    ||||| || |   |  ||  ||  || |  ||||   ||     | | ||| ||       |  |    ||| |   | | ||| |||| ||  |  | || ||  | ||  ||||||||||||| || ||||||||||| || || || ||||||||||| ||||| || || |||| |||||
taaagtttgccaattttatatt-gttccaagtcatttcacctgctgctatttctgtactcttttgtcttttatgattctaatatcaccttttcttctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATCACTGATTTTGAGACCAAGATTAATCTGCTCAAGCTTGCCCATTTTGCGGTGATAGCTTCTC

upper sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
-tgacttttattgaaacaatatttgtactctgata---tgcatgtgttcttattatagtttaaa-tgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC
 |   |||||  |     |||  |  | | ||||    | || || ||  | |   |  ||||  ||| ||  | | | ||     | ||  |  |   |||||||| |||||||| || || || || ||||||||||||||||| ||||||||||| || ||||| ||||| |||||||||||||| |||||  | || ||||
ttaggtttta--gggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttca---tttcagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC

upper sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G19006.1 (Arabidopsis thaliana), 3'ss of exon 1
--tgacttttattgaaacaatatttgtactctgatatgcatgtgttcttattatagtttaaatgtatctgtttcacaaatggttcttcctataaatttt-cagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC
      |||||    |   |||     |  || |  |  |   | | |||      | | |||| |  |||||| |   || || |    ||||  ||| ||||| || ||||| ||||||||  | ||  ||||||||||||| ||||||||||| |  ||||| ||||| ||||||||||||||||||||| |||| || |
cgaatattttagctcagagatacccaaaaactcagctttacaaggt-ttacagatttgttaatg-acgtgtttccccc-tgtttatgttcataatctttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAGACGAGGATCAATCTTCTGAAGCTTGCGCATTTCGCTGTTGTAGTCTCCC

upper sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
-tgacttttattgaaaca-atatt-tgtactctgatatgcatgtgttcttattatagtttaaatgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC
 ||  | ||  |||     || || || | |   ||||   ||  | | |||  |  ||||    |||||     ||  ||  || |   | |  |||| ||||| ||||||||  | || || |||||||| ||||| ||||| ||||||||||| || ||||| ||||||||||| || ||||| ||||| ||||||||| 
ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctt-tttatggttatctaa--aacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA

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|193620586|gb|FK569514.1|FK569514
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTT
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTT
EST: gi|151396447|gb|EV266324.1|EV266324
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|13563374|gb|BG551603.1|BG551603
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|193654585|gb|FK597895.1|FK597895
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTT
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTT
EST: gi|16348793|gb|BI974388.1|BI974388
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|193446598|gb|FK415845.1|FK415845
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTT
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTT
EST: gi|151413131|gb|EV282939.1|EV282939
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|13481959|gb|BG511302.1|BG511302
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|298197844|gb|HO039383.1|HO039383
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|23731463|gb|BU763856.1|BU763856
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|213605649|gb|DB972297.1|DB972297
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|193544951|gb|FK502184.1|FK502184
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTT
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTT
EST: gi|16347671|gb|BI973258.1|BI973258
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|151397751|gb|EV267624.1|EV267624
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
EST: gi|193635103|gb|FK580692.1|FK580692
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTT
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTT
EST: gi|193729324|gb|FK667252.1|FK667252
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACA
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACA
EST: gi|193667524|gb|FK613542.1|FK613542
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTT
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTT
EST: gi|193692521|gb|FK627654.1|FK627654
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCAATTAAATACAATTATATCACAATTT
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCA-TTAA-TACAATTATATCACAATTT
EST: gi|14011491|gb|BG726413.1|BG726413
EST:     ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAG                         GCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG
genomic: ACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttc ... aaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattatagtttaaatgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC
                                                ttttc  CT-rich tract
     atagtttaaatgtat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacttttattgaaacaatatttgtactctgatatgcatgtgttcttattatagtttaaatgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - -gaaacaat
- - - - - - - - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtttc