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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatctcaattaatatacattttttttgtcaatatctattctcaatataaaagaagccaacctcttgtataatatgatttaacaactatgtttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAAGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCCA

Basic information

species Glycine max
transcript GLYMA14G40320.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 7
aaatctcaattaatatacattttttttgtcaatatctattctcaatataaaagaagccaacctcttgt-ataatatg-atttaac---aactatgtttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAAGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCCA
     |        | | ||| |  |     | |||| || |  | |    |   |   | || ||||  | | | |  |||||    ||||   ||||    |||| ||||| ||||  |||||||| || || ||||||||||||||| | ||| ||| ||| || |||||||| || || || |||||||| |||||  | |
-----ttgggctggacatattatactgaaacacatctcttatatagaccttatttgtgcatctgttgttgttacaagtgtttaattcgaactcacttttatgtagGATTTGGTTAAGAAGTACTCTGAGTTCATCAACTTCCCTATCTATTTGTGGTCAACCAAGGAGGTTGATGTTGAAGTGCCAGCTGATGAGGATGAGACAA

upper sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 7
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 7
-----aaatctcaattaatatacattttttttgtcaatatctattctcaatataaaagaagccaacctcttgt-ataat-atgatttaacaactatgtttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAAGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCCA
        ||   |||| |||  |||   |    || |   |||||  |||||    |     | |||||  | ||  |    | | | ||    ||| |   ||||||||||||||||||||| |||||||| ||||||||||||||||   | ||||| |||||||| |||||    ||||| || | ||| |||||||| ||  
gaagtggttcagcattattatgaattcagt---gcactgcttattc--aatatttctgt--ttatcctctcattatggttgctaatgatcattgttgtctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGGGCTAGCAAAGAGGTTGAAACCGAGGTCCCAGTTGAGGAAGATGAATCAG

upper sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 7
aaatctcaattaatatacattttttttgtcaatatctattctcaatataaaagaagccaacctcttgtataa---tatgatttaacaactatgtttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAAGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCCA
|  |     ||  | |  ||||||    | |||||     |   ||      || |  ||  ||| || ||    | | ||||  | ||  || |  |   |||| || ||||| ||||| |||||||| || ||||| || || ||  | |||||||||||||| |||||||| ||||| || || ||||||||||| || |
agttaatttttgctttttatttttccaatgaatatgggagc---attcttgtgatgtaaatatctggtttaggtttttaattttgctaccttgataattgtagGAGTTAGTGAAAAGATATTCTGAATTCATCAACTTTCCCATATACCTCTGGGCAAGCAAAGAGGTTGATGTAGAGGTACCTGCAGATGAAGATGAGTCAA

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|57574607|gb|CX547582.1|CX547582
EST:     TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAA                         GAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
genomic: TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
EST: gi|298173461|gb|HO016797.1|HO016797
EST:     TGGGGAATACTTGGAGGAGTCTAAACTGAAA                         GAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
genomic: TGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
EST: gi|58019806|gb|CX706548.1|CX706548
EST:     ACACNNTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAA                         GAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
genomic: ACAC-CTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
EST: gi|163922973|gb|EH039569.1|EH039569
EST:     TACACCTCAAGGAAGAGGCTGGGGAGTACTTGGAGGAGTCTAAACTGAAA                         GAATTGGTGAAGAGATACTCTGGATTTATTAACTTCCCTATCTATATTTGG
genomic: TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
EST: gi|298194890|gb|HO043362.1|HO043362
EST:     TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAA                         GAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
genomic: TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
EST: gi|193663124|gb|FK601014.1|FK601014
EST:     TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAA                         GAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
genomic: TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
EST: gi|193710049|gb|FK643349.1|FK643349
EST:     TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAA                         GAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
genomic: TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
EST: gi|207817171|gb|GD786374.1|GD786374
EST:     GGCTGGGGAATACTTGGAGGAGTCTAAACTGAAA                         GAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
genomic: GGCTGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
EST: gi|208219473|gb|GE020571.1|GE020571
EST:     TACACCTCAAGGAAGAGGCTGGGGAGTACTTGCAGGAGTCTAAACTGAAA                         GAATTGGCGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
genomic: TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
EST: gi|254328195|gb|GR835160.1|GR835160
EST:     TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAA                         GAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG
genomic: TACACCTCAAGGAAGAGGCTGGGGAATACTTGGAGGAGTCTAAACTGAAAgtatacatca ... tttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataaaagaagccaacctcttgtataatatgatttaacaactatgtttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAAGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCCA
                               atttaac  putative branch site (score: 3)
                                           tgtttttc  putative PPT
                      tataatatgatttaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatctcaattaatatacattttttttgtcaatatctattctcaatataaaagaagccaacctcttgtataatatgatttaacaactatgtttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAAGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - aaaagaa