Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatcacaacagtttctgtttatctgttatactgccattattttcttgtttagcctttaaaggaaaccataactaaactttgaatgtcactggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG

Basic information

species Glycine max
transcript GLYMA10G35230.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 2
ttaatcacaacagtttctgtttatctgttatactgccattattttcttgtttagcctttaaaggaaaccataactaaactttgaatgtcactggaa--acagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
    | ||  ||  || ||     || |  |||| | || ||     | | |    || |   | | |  |   |||  | |  ||     ||       || | ||  |  | ||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||
--gtttactgcacattttgcc---ctttattactacaataatgcctctatatcatgtt-actagcagctttctttaacgtgtccatccttttgatgttgtagTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 3'ss of exon 2
--------ttaatcacaacagt--------ttctgtttatctgttatactgccattattttc-ttgtttagcctttaaaggaaa----ccataactaaactttgaatgtcactggaa---acagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
        ||| |||| |  ||        |||| || || | |   |   ||||| ||  | ||   | |  ||  || ||||     |||  |     |||  || | ||   |      || | ||  |  | || ||||| |||||||| ||||| || |||||||| || ||||| |||||||||||||| || || || |||
gtttggacttactcactagtgtcttcataattcttttaatatttctcatctccattgttgacattaagttgaattggaatgaaaaggttcatgcccttcgtttttattttaccctattctgtagTTGGTATTGCTTGGAGATTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGCTTTGTCCGTGGTCAGTTTGACCCCACTTCAAAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 3
ttaatcacaacagtttctgtt-tatctgttatactgccattattttcttgtttagcctttaaaggaaaccataactaaactttgaatgtcactggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
|   | |   ||   |   |  |  |||| ||    | | ||    ||   |      |||| |       | | |    ||  |   || |  |  | || | ||  |  | || || || |||||||| ||||| || |||||||| || ||||||||||||||||||||||| || || |||
tatgttagggcatcattaatagtggctgtgatttatctagtaaaacctgaatacctgattaacgacttttgttaatgt-tttcaaccttctcatgttatagTTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 2
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
ttaatcacaacagtttctgtttatctgttatactgcca----ttattttcttg-tttagcctttaaaggaaac-cataactaaactttgaatgtcactggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
||| |  |     ||  || | | | || ||  |||||    |  | |  ||| |||   ||||     | ||  |  |||||  |||| ||     ||    ||| | ||||| ||||| || ||||||||||||||||| |||||||| || |||||||| ||||||||||||||  | |||||||||
ttattttc-----ttgttgctcagcagt-attttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
ttaatcacaacagt-ttctgtttatctgttatactgccattattttcttgtttagcctttaaaggaaaccataactaaactttgaatgtcactggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
 |      || |   || |    ||   ||     || | |||    |||  ||        |    |    | ||   ||| |    ||| ||    ||||| ||| | || || |||||||||||||| ||||||||||||||||| || ||||||||||| |||||||| || ||||| |||
ctgcaagaaatatcattatagaaattaattgatgggcaaatataggattgaataagaaccctaaattatttcagctct-cttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG

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|5605755|gb|AI899819.1|AI899819
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|193543327|gb|FK502506.1|FK502506
EST:     AATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: AATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|193724791|gb|FK658075.1|FK658075
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|15813084|gb|BI785359.1|BI785359
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|308098577|gb|HO760318.1|HO760318
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|298165609|gb|HO011658.1|HO011658
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTGCGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|298183380|gb|HO028593.1|HO028593
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|7286166|gb|AW598653.1|AW598653
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|298177777|gb|HO027330.1|HO027330
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|298182667|gb|HO031402.1|HO031402
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|298185154|gb|HO030367.1|HO030367
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|15201204|gb|BI424748.1|BI424748
EST:     CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
EST: gi|298174351|gb|HO017687.1|HO017687
EST:     CCAATTCAGAGAATGGTGGAGGACAGGACGCCAAGAATCTGAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAGgtatttgtgt ... ctggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttagcctttaaaggaaaccataactaaactttgaatgtcactggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
                          aactaaa  putative branch site (score: 2)
                        ataactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatcacaacagtttctgtttatctgttatactgccattattttcttgtttagcctttaaaggaaaccataactaaactttgaatgtcactggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG

- - -cacaaca
- - - - - - gtttctg
- - - - - - - - - - - - - - - - ctgccat
- - - - - - - - - - - - - - - - - - - - - - - - - - -gccttta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgt