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

gtaatgctttgaattacaaacatctgtagttatgccctctgccatatttttctgttaagtattggttttctaactgtttacatcacggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTATGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG

Basic information

species Glycine max
transcript GLYMA17G13640.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13640.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g40850.2 (Oryza sativa), 3'ss of exon 3
gtaatgctttgaattacaaacatctgt-agttatgccctctgccatatttttctgttaagtattg-gttttctaactgtttacat---------cacggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTATGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG
|||| |     | |  |  |  | ||| | ||||    | |  | | ||||| ||||  | |||  | | |||||   || |||          |  | | | || ||||||||||| |||||||||||||| |||||||| ||  |||||||||| || ||| | ||||||||| ||||| |||| |||||||| ||||| |  
gtaa-gtccgaagtctctcatttttgttatttataatgttttgcttgtttttttgttttgcattatgatgtctaatacttcacaaatttgttggctggattgaagATTGTTTGAGGAGGGTGGTGATTGGGAGAGGAAGAACAGATTGAAAGTGTACGAGGGCTTATACTGCATGGCCACTAGAAACTTCAAGAAAGCTGCAAGC

upper sequence: GLYMA17G13640.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G093557_T02 (Zea mays), 3'ss of exon 4
gtaatgctttgaattacaaacatctgtagttatgccctctgccatatt---tttctgttaagtattggttt---tctaactgtttacatcacggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTATGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG
         | |||   ||   | | |  ||   | |     || |||   |||  |||  | |   | |    || |||  | |   ||  | | | |||||||||||||||||||||||||||||||||||||| ||  ||||||| ||||||||  ||||||||||| | ||| |||| |||||||| ||||| |  
--------gtaaatccaaattctttttgatttatctcctcttcaaattggatttgcgttgtgaagctgataaagtccaacattgtttctcctgattgaagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAACAGATTGAAAGTATATGAAGGGTTGTACTGCATGGCAACTAGAAACTTCAAGAAAGCTGCTAGT

upper sequence: GLYMA17G13640.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G029583_T03 (Zea mays), 3'ss of exon 4
gtaatgctttgaattacaaacatctgtagttatgccctctgccatatttttctgttaagtattggt--tttctaactgtttacatcacggtg-gcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTATGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG
|||| ||| |   ||       |||| |||| |    ||||  || |       |  |||   |||  ||| | ||  | ||  |||| ||  | ||||||||||||||||| || |||||||| |||||||| ||| ||||||| ||||||||| ||||||||||| | ||  |||| |||||||| |||||||  
gtaa-gctctatctt-----tgtctgcagttctaa--tctgtaat-tcggcacatagagttagggtgatttttgaccatatatttcactgtctgaagCTTGTTTGAGGAAGGAGGCGATTGGGAGAGGAAGAACAGGTTGAAAGTATATGAAGGCTTGTACTGCATGGCAACCAGAAACTTCAAGAAAGCTGCCAGC

upper sequence: GLYMA17G13640.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g10250.t01 (Vitis vinifera), 3'ss of exon 4
--gtaatgctttgaattacaaacatctgtagttatgccctctgccatat------ttttctgttaagtattggttttctaactgtttacatcacggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTATGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG
   |  | |||| ||| | |    |||    || ||  |      | |           || | |  |  | ||||||||| |||||| | || ||  ||||||||||||| || || ||||||||||||||||||||  |  |||| |||||||||||||||||||||||||||||| |||| ||||||||||| ||||| 
cttttcttcttttaat-atatttttcttcgtttctgatcaaaaaaaaaaaaaataccacctttgatttgcttgttttctaattgttta-aacatggatgcagCTTGTTTGAAGAGGGAGGTGATTGGGAAAGGAAGAACCGTTTGAAGGTGTATGAAGGCCTGTACTGCATGTCCACTAGAAACTTCAAGAAGGCAGCCAAT

upper sequence: GLYMA17G13640.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ25080 (Selaginella moellendorffii), 3'ss of exon 4
gtaatgctttgaattacaaacatctgtagttatgccctctgccatatttttctgttaagtattggttttctaactgtttacat-cacggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTATGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG
                                        |    || ||| ||   | | || |||| ||      | ||||    |    ||||||||| ||||| || ||||| ||||||||||||||  | |||||||| || || || || ||||||||| | || || || |||||||| |||||  ||
----------------------------------------gtgggatgtttgtg---attttttgtttacttggaactgacatgtttgacctcagCTTGTTCGAGGAGGGCGGTGACTGGGAAAGGAAGAACCGCCTGAAAGTTTACGAGGGGCTCTACTGCATGGCGACCCGGAACTTCAAGAAAGCTGCGGAG

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|151402130|gb|EV271943.1|EV271943
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|151395478|gb|EV265355.1|EV265355
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|15285764|gb|BI469655.1|BI469655
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|57574692|gb|CX547667.1|CX547667
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         C-TGTTTGAGGAAGGTGGTGATT-GGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|9204415|gb|BE330639.1|BE330639
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|15200697|gb|BI424483.1|BI424483
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATACGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|193622859|gb|FK571115.1|FK571115
EST:     TTGACANGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGACC-AAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGT
genomic: TTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAG-CCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGT
EST: gi|120494667|gb|EH222834.1|EH222834
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|151393805|gb|EV263680.1|EV263680
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|193343674|gb|FK313142.1|FK313142
EST:     ACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: ACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|16346992|gb|BI972587.1|BI972587
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATANGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|151407732|gb|EV277547.1|EV277547
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|254314141|gb|GR831770.1|GR831770
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAACGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|24205374|gb|BU964627.1|BU964627
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|15814441|gb|BI786716.1|BI786716
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTG
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTG
EST: gi|18039910|gb|BM308204.1|BM308204
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTA
EST: gi|208140365|gb|GD936975.1|GD936975
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGT
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGT
EST: gi|16996806|gb|BM086169.1|BM086169
EST:     TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGTGGTGATTGGGGAAGGAAGAATAGGCTGAAA
genomic: TTTGACATGGATTTTGATCTCATTTCCAAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAA
EST: gi|58016465|gb|CX703207.1|CX703207
EST:     TCATTTCCAAAAAGCATAGACAAAGCCAAAAA                         CTTGTTTGAGGAAGGT-GTGATTTGGAAAAGGAAGAATAGGCTGAAAGTGT
genomic: TCATTTCC-AAAAGCATAGACAAAGCCAAAAAgtaatgcttt ... acggtggcagCTTGTTTGAGGAAGGTGGTGA-TTGGGAAAGGAAGAATAGGCTGAAAGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccatatttttctgttaagtattggttttctaactgtttacatcacggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTATGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG
                            ttctaac  putative branch site (score: 1)
     tatttttctgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgctttgaattacaaacatctgtagttatgccctctgccatatttttctgttaagtattggttttctaactgtttacatcacggtggcagCTTGTTTGAGGAAGGTGGTGATTGGGAAAGGAAGAATAGGCTGAAAGTGTATGAAGGCCTGTACTGCATGTCCACTCGAAATTTCAAGAAGGCTGCCAAG

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