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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctcttttccagataatgtgcttgtttttttatatgctgcatgaataacaggctatatgcaggttcagtaatttatgctttttgtgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGACTACCCAGAAAAGCCCCCAAGTGTTCGGTTTCATTCACGAATCAATATGA

Basic information

species Glycine max
transcript GLYMA03G35790.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G35790.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 2
-tatctcttttccagataatgtgcttgtttttttatatgctgcatgaataacaggctatatgcaggttcagtaatttatg-ctttttgtgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGACTACCCAGAAAAGCCCCCAAGTGTTCGGTTTCATTCACGAATCAATATGA
     | | |    ||||   |  |     |  | |||  || ||    |      || || ||| ||   |  |   |  || |||   ||  | |  ||| |||||||||||||  | ||||||||| ||||| | |||||||||||||| || || || ||||| || ||||| ||||| |||||||| ||||| ||||
aagattttgtgtttgatagcttattc--catcgtgtatcatgtattctcacatctatacatacagattttatgttcattaactattttaattactttttcagTCTGTACATGAAGGTCGCATTTATCAACTGAAGCTTTTTTGTGATAAAGATTATCCGGAGAAGCCTCCTAGTGTACGGTTCCATTCACGCATCAACATGA
















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|298170909|gb|HO015885.1|HO015885
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGCTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|13789951|gb|BG652542.1|BG652542
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|298192803|gb|HO033237.1|HO033237
EST:     GCGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|298191462|gb|HO038941.1|HO038941
EST:     ACGACATTTACATGCGCTCTTGGACTGGGACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGA
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGA
EST: gi|6072466|gb|AW101853.1|AW101853
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|192315721|gb|FK011189.1|FK011189
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|10236212|gb|BE805100.1|BE805100
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|298189032|gb|HO035669.1|HO035669
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|15815632|gb|BI787907.1|BI787907
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|11412512|gb|BF424523.1|BF424523
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|15199562|gb|BI423894.1|BI423894
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGGTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|8827283|gb|BE211013.1|BE211013
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|16995653|gb|BM085025.1|BM085025
EST:     ACGACATTTACATGCGCTCTTGGACTGTAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|9819988|gb|BE555501.1|BE555501
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|13791117|gb|BG653708.1|BG653708
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|9900279|gb|BE609247.1|BE609247
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|12773589|gb|BG238516.1|BG238516
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|21594189|gb|BQ610071.1|BQ610071
EST:     ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: ACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
EST: gi|6718534|gb|AW306181.1|AW306181
EST:     CGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCCTATAAT                         ACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC
genomic: CGACATTTACATGCGCTCTTGGACTGGAACCATTATTGG-CCCCTATAATgtaaatattt ... tttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataacaggctatatgcaggttcagtaatttatgctttttgtgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGACTACCCAGAAAAGCCCCCAAGTGTTCGGTTTCATTCACGAATCAATATGA
 gaataac  putative branch site (score: 2)
                                  ctttttgtgtttttct  putative PPT
                         taatttatgcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatctcttttccagataatgtgcttgtttttttatatgctgcatgaataacaggctatatgcaggttcagtaatttatgctttttgtgtttttctaccagACTGTACATGAAGGAAGAATTTATCAATTGAAGTTGTTTTGTGATAAAGACTACCCAGAAAAGCCCCCAAGTGTTCGGTTTCATTCACGAATCAATATGA

- - - - - - - - - - tgcttgt
- - - - - - - - - - - - - - - - tatatgc
- - - - - - - - - - - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaggt