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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatcattagaataatcttaattttgttttttttttatctaagccatgtatttgtgataataataactttgttttgattttatatttttggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG

Basic information

species Glycine max
transcript GLYMA04G42830.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 3'ss of exon 4
ttaatcattagaataatcttaattt-tgttttttttttatctaa-gccatgtatttgtgataataataactttgttttgattttatatttttggtacga-cagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
|| || ||    ||  | | | ||| |    | |  | || ||  ||| ||| ||| |  |  |||    ||  |  | ||   |  |  ||  |   | ||||||||| || ||||||||||| ||  |||||||||| || || || || ||||||||||||||||| |||| ||||||   ||||
ttgatgatacctatcttttcactttgtaccatatgctgatttactgccttgt-tttatatttttaagg--ttcatactaatcaaaggtgattcttgtaagcagGGAACTAGCGAAAGATTTTGTGGTTTCTGGCACTGCTTCAGAATCACTATATGGTGCTTGTGAGTCCATGTATAAGCCAAGCATG

upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g43570.1 (Oryza sativa), 3'ss of exon 5
ttaatcattagaataatcttaattttgttttttttttatctaagc-catgtatttgtgataataataactttgt--tttgattttatatttttggtacga--cagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
       || |  |||       |   |  | | | |   || ||   || |    || |  | |||   ||||    |||||    || |||  | |    ||||||||| || || ||||| || ||  | || || ||||| |||||||| ||||||||||||||||| ||||  || ||  |||||
-----ttttggtctaagtccgtgtgcctgatatgtctgattaggcgtttgaacgcttgtttctcatattcttgtgagctgattgaggatgtttatttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATATGGTGCTTGTGAGTCCATGTACAAACCAAACATG

upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G117544_T02 (Zea mays), 3'ss of exon 3
ttaatcattagaataatcttaatt--ttgttttttttttatctaagccatgtatttgtgataataataactttgttttgattttatatttttggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
 ||||  |||      |   ||||  ||  ||   |  |||     |     || ||   |    |     |  | ||       |||||    |    ||||||||| |||||||||||||| ||  | || ||||| || ||||| |||||||||||||||||||| |||| ||||||  |||||
-taat-gttaagcctgttgaaattcgttccttacatcctatactgacttgccatatggcctctctaccttgtaatcttatcagagtatttccttttattcagGGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG

upper sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 4
----ttaatcattagaataatcttaattttgttttttttttatctaagccatgtatttgtgataataataactttgttttgattttatatttttggtacgac-agGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
     | || || ||  | |||  |  ||| |||||   | || |   |  | |    ||| |  ||   | |||  ||| |||||   | ||    ||  | ||||| ||||| ||||||||||| || ||||| ||||| || ||||||||||||||||| || ||| | ||||| ||||| ||||||
ttgtctgattat-aggttgatccaagctttctttttgggtgatattgacattatg---gtgctt-tacctaattttctttaatttttcttcttcctcacatccagGGAGCTTGCTAAAGATTTTGTTGTTGCTGGTACTGCCTCTGAGTCTCTTTATGGTGCCTGCGAGGCCATGTTCAAGCCCGACATG

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|16343834|gb|BI969429.1|BI969429
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|16996875|gb|BM086247.1|BM086247
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|214005797|gb|DB985945.1|DB985945
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|298166167|gb|HO009138.1|HO009138
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGGACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|298176811|gb|HO023284.1|HO023284
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|16348632|gb|BI974227.1|BI974227
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|8401459|gb|BE057093.1|BE057093
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTGTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|192322314|gb|FK014555.1|FK014555
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|192325513|gb|FK018424.1|FK018424
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|151409085|gb|EV278893.1|EV278893
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|7588098|gb|AW703901.1|AW703901
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|17963651|gb|BM270398.1|BM270398
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|8283379|gb|BE020940.1|BE020940
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|298178421|gb|HO024156.1|HO024156
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTCGCAAAAGATTTTGTAGTGGCTGGCACAGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|298189628|gb|HO038031.1|HO038031
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|213605503|gb|DB968761.1|DB968761
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|6567370|gb|AW234981.1|AW234981
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|151397166|gb|EV267039.1|EV267039
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|151411912|gb|EV281723.1|EV281723
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
EST: gi|16343936|gb|BI969531.1|BI969531
EST:     GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA                         GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA
genomic: GGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaa ... ggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtatttgtgataataataactttgttttgattttatatttttggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG
     atttgtgataataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatcattagaataatcttaattttgttttttttttatctaagccatgtatttgtgataataataactttgttttgattttatatttttggtacgacagGGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATG

- - - - - - - - - - - - - - - - - - - - - - ccatgta