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

...tcgacaaatgttagtttgttggagtgtcagttttgttaatagagaggatcaagatctttaatgaaagtgacataatgtaggcaagtatttgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA

Basic information

species Glycine max
transcript GLYMA04G42010.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
tcgacaaatgttagtttgttggagtgtcagttttgttaatagagaggatcaagatctttaatgaaagtgacataatgtaggca----agtatttgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA
|  |  |   |   ||| |||   | | ||  |  |   |   |      |        || | || ||    | |||   ||    |   |||| ||||||||||||||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| | ||| |  |    
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT----

upper sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
tcgacaaatgttagtttgttggagtgtcagttttgttaatagagaggatcaagatctttaatgaaagtgacataatgtaggcaagt----atttgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA
      |   |   ||| |||   | | ||  |  |   |   |      |        || | || ||    | |||   || |      |||| ||||||||||||||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| | ||| |  |||||
----gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaaaggaactgctggattgttttcatgatatagtttgttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA

upper sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
tcgacaaatgttagtttgttggagtgtcagttttgttaatagagaggatcaagatctttaatgaaagtgacataatgtag-gcaagtatt-tgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA
   | |||| ||      |||||   | | | |||    |  |      ||  ||  |   ||  | |    |  ||||  | || | |  || ||||||||||||||| || || || || || || |||||||||||||| ||||||||||| |||||||||||||| || |||  |||    || ||| |||| ||| |
--cataaatctttaggctttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA

upper sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g15360.t01 (Vitis vinifera), 3'ss of exon 1
--tcgacaaatgttagtttgttggagtgtcagttttgttaatagagaggatcaagatctttaatgaaagtgacataatg-taggcaagtatttgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA
     ||  |  |||    | |  ||   ||  |  || | |        ||    |  | ||   || || ||   || |  | ||  || || |||||||||||||||||| || || || |||||||| || || ||||| |||||||||||||||||||| |||||||| |||| |||   ||| |||   |  |||||
ttgaaacttaaattaacaagctaaag---caactgggtcacttagagctctctctgttgtaaagtgaactgtcaccttgattagtaaagatgtgctcagacagGTTGGAGGACATACCGGAGACCGGATGAAAAATCTGGAGGCCATGGTGTTGGATGGAGTCCGATTATTCCTTACATCTTTTCAGTCCCTTCTGGTTGGGA

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|151399188|gb|EV269059.1|EV269059
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         A
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacag-
EST: gi|151399188|gb|EV269059.1|EV269059
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         A
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacag-
EST: gi|151399188|gb|EV269059.1|EV269059
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         A
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacag-
EST: gi|151399188|gb|EV269059.1|EV269059
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         A
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacag-
EST: gi|24205729|gb|BU964982.1|BU964982
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         A
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacag-
EST: gi|24205729|gb|BU964982.1|BU964982
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         A
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacag-
EST: gi|24205729|gb|BU964982.1|BU964982
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         A
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacag-
EST: gi|24205729|gb|BU964982.1|BU964982
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         A
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacag-
EST: gi|10231586|gb|BE800474.1|BE800474
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         GTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAG
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAG
EST: gi|209716366|gb|BW657486.1|BW657486
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         GTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTG
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTG
EST: gi|151397074|gb|EV266947.1|EV266947
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         GTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTG
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTG
EST: gi|151402608|gb|EV272421.1|EV272421
EST:     AGGCCTTCTAGCAGGGAGAATTCCCGGCCTGTCCGAGCCAGGTGAACAAG                         GTTGGAGGACCTATCGCAGGCAGGATGAGAAGTCAGGAGGACATGGTGTTG
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTG
EST: gi|5510308|gb|AI856750.1|AI856750
EST:     AGGCCTCCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         GTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTG
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTG
EST: gi|213594235|gb|DB966136.1|DB966136
EST:     AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAG                         GTTGGAGGACCTATCGCAGGCCGGATGAGAA-TCAGGAGGACATGGTGTTG
genomic: AGGCCTTCTAGCAGGGAGAATTCCTGGCCTGTCCGAGCCAGATGAACAAGgttcgttcat ... gatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatcaagatctttaatgaaagtgacataatgtaggcaagtatttgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA
           tttaatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgacaaatgttagtttgttggagtgtcagttttgttaatagagaggatcaagatctttaatgaaagtgacataatgtaggcaagtatttgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - -tggagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaagta