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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatgcattgttagtaattctttttatagtgaacctttatttgtattgaaggtttttaggattcatataggtgctgatgattttgtaaatatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTGACATGAGGGGACTAGCTGGAGGCTTGAATGGGCTAAACACTTCAGCCAT

Basic information

species Glycine max
transcript GLYMA06G38160.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G38160.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G54190.2 (Arabidopsis thaliana), 3'ss of exon 2
ataatgcattgttagtaattctttttatagtgaacctttatttgtattgaaggttt---ttaggattcatat---aggtgctgatgattttgtaaat-atcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTGACATGAGGGGACTAGCTGGAGGCTTGAATGGGCTAAACACTTCAGCCAT
          ||  ||| |    |    ||   |    | | |||| | |    ||    ||      | ||   |  |  |  |  ||||||   | ||  | |||||||||| || ||||||||||| ||||| || || |||||||| ||||||||  ||||||||||||| || || ||||| ||||||||||  || || ||
----------gtctgtagtctcctcataagaagaatgctttatgtacttactacttactctaaaccctaaatctgaaatcttattcgttttgtttcttattgagcagGAAACACTAATACATTGGCTGGTAATGTACCTCCAAAGGCTAATCTTGGTGATTTGAGGGGACTAGCAGGCGGGTTGAACGGGCTAAACAGCTCGGCGAT

upper sequence: GLYMA06G38160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0014g03160.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------ataatgcattgttagtaattctttttatagtgaacctttatttgtattgaaggtttttaggattcatataggtgctgatgattttgtaaatatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTGACATGAGGGGACTAGCTGGAGGCTTGAATGGGCTAAACACTTCAGCCAT
                                  |||   |    ||  | |   ||| ||  |||   |  ||    |||   |   | ||    |  ||    ||||  |  || | |||| || || |||| ||||| || || ||||||||||||||||| || ||||| |||||||| ||| |||||||| | || |||||  | |||||||| ||||  ||||||||
gtactgcaattaatcaggacaaatatgattcatgtaaaatagaagtaccactgaatttcatgatgagt-tcaatacaaatt--tgtcatataaatgtactaagtatgctattccttctataaa-atgaatcagGGAACACAAATACCTTGGCTGGAAATGTGCCTCCAAAGGCCAACCTTGGGGACTTGAGGGGAATGGCAGGAGGTCTAAATGGGCTGAACAGCTCAGCCAT
















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|7692645|gb|AW760746.1|AW760746
EST:     CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|6454735|gb|AW185418.1|AW185418
EST:     CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|192309153|gb|FG999086.1|FG999086
EST:     CAAATCTGACTACCCTTCGAGGCGGTTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|193494044|gb|FK462670.1|FK462670
EST:     CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|8404313|gb|BE059947.1|BE059947
EST:     CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|192307156|gb|FK002304.1|FK002304
EST:     CCTTCGAAGCGG-TGATCATTGTAGGCTC-ATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAA-CTTGGTG
genomic: CCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|12690020|gb|BG156356.1|BG156356
EST:     CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|117557761|gb|EG702146.1|EG702146
EST:     CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|8404324|gb|BE059958.1|BE059958
EST:     GCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: GCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|15286523|gb|BI470414.1|BI470414
EST:     CAAATCTGACTACCCTTCGAAGCGGNTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|15203279|gb|BI426047.1|BI426047
EST:     CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|7146781|gb|AW508703.1|AW508703
EST:     CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: CAAATCTGACTACCCTTCGAAGCGGTTGATCATTGTAGGCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
EST: gi|192297103|gb|FG988199.1|FG988199
EST:     GCTCAATCACAG                         GAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG
genomic: GCTCAATCACAGgtataactca ... tatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaaggtttttaggattcatataggtgctgatgattttgtaaatatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTGACATGAGGGGACTAGCTGGAGGCTTGAATGGGCTAAACACTTCAGCCAT
                           tgctgat  putative branch site (score: 3)
                                   attttgtaaatatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatgcattgttagtaattctttttatagtgaacctttatttgtattgaaggtttttaggattcatataggtgctgatgattttgtaaatatcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTGACATGAGGGGACTAGCTGGAGGCTTGAATGGGCTAAACACTTCAGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- aatgcat
- - - - - - - - - - - - - - agtgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat