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

GAGAAAGCTCCATATGAAGCCAAGGCTGCGAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacctgtgccagtttttctgttgtgtgtggcactttgattgtcttgtgtttatatactttattttctataatgttgccag

Basic information

species Glycine max
transcript GLYMA03G08270.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G08270.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G51880.1 (Arabidopsis thaliana), 5'ss of exon 6
GAGAAAGCTCCATATGAAGCCAAGGCTGCGAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacctgtgccagtttttctgttgtgtgtggcactttgattgtcttgtgtttatatactttattttctataatgttgccag
|| ||||||||||||||||  || ||||| |||||||||||||| ||||| || |  ||  | || ||  | |||||   ||| ||   |||  |||  ||  |||  | | |         |   |  ||     | || | | ||    |    ||         
GAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTGgtaagc--cctaagcc--ttactctcatatatacaaactcgtacatagctaactctgat-ttccttgcaatggggaacag------

upper sequence: GLYMA03G08270.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv08s0007g02200.t01 (Vitis vinifera), 5'ss of exon 6
GAGAAAGCTCCATATGAAGCCAAGGCTGCGAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacctgtgccagtttttctgttgtgtgtggcac----tttgattgtcttgtgtttatatactttattttctataatgttgccag--
|| |||||||||||||| ||||| ||||| |||| ||| |||||||| |||||| |||| || |||||  | || |||||||| |  | | ||    ||  ||| | |  |    |  |      || |||| |  |   | |  | | | | ||||| |  ||||       
GAAAAAGCTCCATATGAGGCCAAAGCTGCAAAAAAGAAGGCTGAGTACGAAAAAATTATGAATGCTTACAACAAGAAGCAGgtgaaca-catgcataagcctttttctcatcaaagaaatgattcttcattgcc--gatatcacttgcctgactttcttttgtgttattgcag
















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|193433075|gb|FK398723.1|FK398723
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|193362709|gb|FK324385.1|FK324385
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|22524201|gb|BU083012.1|BU083012
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACNAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|14125883|gb|BG790321.1|BG790321
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|4294807|gb|AI442243.1|AI442243
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCCTTCG-AGATGATGAAGA
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGC-TCCGCAGATGATGAAGA
EST: gi|8284057|gb|BE021616.1|BE021616
EST:     ATAGGATAGCTGAGTATGAAGAACTTATCATAGCTTATGATAAAAAGCAT                         GCAAGCTCCGCAGATGATGAAGA
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGA
EST: gi|15204898|gb|BI427666.1|BI427666
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|193360121|gb|FK327243.1|FK327243
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|298196480|gb|HO041223.1|HO041223
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|26057109|gb|CA800023.1|CA800023
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAG
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAG
EST: gi|20814222|gb|BQ298700.1|BQ298700
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|22522971|gb|BU081782.1|BU081782
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|20075624|gb|BQ094407.1|BQ094407
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
EST: gi|208047248|gb|GD844345.1|GD844345
EST:     AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG                         GCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT
genomic: AAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacc ... atgttgccagGCAAGCTCCGCAGATGATGAAGAATCAGACAAGTCCAAATCTGAAGTGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAAGCTCCATATGAAGCCAAGGCTGCGAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAGgtcagtaacctgtgccagtttttctgttgtgtgtggcactttgattgtcttgtgtttatatactttattttctataatgttgccag

- - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - AGCTGA