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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaactagtttgccaatacatatactcctattattagtccctgatacaaacttgataataaattcctaatttagatttatggatttgtaattgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA

Basic information

species Glycine max
transcript GLYMA03G35790.1
intron # 3
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 3
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 3
atgaactagtttgccaatacatatactcctattat-tagtccctgatacaaacttgataataaattcctaatttagat--ttatggatttgtaattgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA
   || |  ||  |  || | |  | ||| | | | | |  | | | |    ||   ||  |  | |||     || |  | ||||| |   | |     ||||||||| ||||||| |||||  | || ||||||||||| |||  ||| || |||||||| ||| |||| ||||||||||| |||||||| ||  | || |
---aaatctttgtcatattcctgaattccaaatttatggatcattaaaaggtctcagtacgagttgccttgcaaagctaatgatggagtccgattgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACAATGGAAGACATATTGACGCAGCTGAAGAAAGAAATGGCAGCCCCCCACA
















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:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGACAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|13789951|gb|BG652542.1|BG652542
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|298192803|gb|HO033237.1|HO033237
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|6072466|gb|AW101853.1|AW101853
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|192315721|gb|FK011189.1|FK011189
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|10236212|gb|BE805100.1|BE805100
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GCTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCATCGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|298189032|gb|HO035669.1|HO035669
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|15815632|gb|BI787907.1|BI787907
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GCTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCCACGGAGGCTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|11412512|gb|BF424523.1|BF424523
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCCAATTGGCAACGGGGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|15199562|gb|BI423894.1|BI423894
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|8827283|gb|BE211013.1|BE211013
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|16995653|gb|BM085025.1|BM085025
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|9819988|gb|BE555501.1|BE555501
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GCTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGGTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|13791117|gb|BG653708.1|BG653708
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|9900279|gb|BE609247.1|BE609247
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|12773589|gb|BG238516.1|BG238516
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|21594189|gb|BQ610071.1|BQ610071
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
EST: gi|105637981|gb|DY577264.1|DY577264
EST:     GGTTTCATTCACGAATCAACATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAA
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAA
EST: gi|6718534|gb|AW306181.1|AW306181
EST:     GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC
genomic: GGTTTCATTCACGAATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtatgattct ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaaacttgataataaattcctaatttagatttatggatttgtaattgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA
                   tcctaat  putative branch site (score: 2)
       ttgataataaattcct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaactagtttgccaatacatatactcctattattagtccctgatacaaacttgataataaattcctaatttagatttatggatttgtaattgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - -tgccaat
- - - - - - - - - -catatac
- - - - - - - - - - - - - - - - - - - tccctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatttg