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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA

Basic information

species Glycine max
transcript GLYMA12G30910.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
-cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcat-cagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
   || |  | || |  ||      | | ||   | ||  || |   |   |      | || || |   | |  |  || | | | |  | ||| || |||| | ||||||||||||||||||||||| |||||||| || |||||||| || ||| ||||||||||| |||||||||||||||  || ||||| || || 
tgatgttgccaatgatcaatatcaatgtataccat-attcatttgtattgttcgtgcaatatattttattatgtttcatttaatgt-gtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
 |   | ||| ||       |    |  || |  ||     ||| |        |     | |  ||      || || |   |||   || |    |||  | ||||||||||||||||||||||| |||||||| |||||||| || || ||| | || |||||| | ||||| || |||| ||| || || || || 
ttctctttcttttctttgctgctactgctagtactagtgcagtatgctttgttctttgtttctgtttcatgttatgttaacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 2
-----cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
     ||||||     | ||   | ||      || |  |||      |  |   |     | | | |  ||   |  ||||   ||| |||   | | |  |||| | ||||| ||||| || |||||||||||||||||||||||||| ||  | ||| |||| || ||| |||||||||| |||| ||||||||| || || 
tttcacttgat--tggtcaatggatgttagcaatactaatatcctaccatttgttttctatgccgtatctttatga-tatttcacactgttg--ctttactgcagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGTGAGAAATTAGTTGCAAATCTGTTCCAAATGGCTCGGGAAAATGCCCCTTCCATTATC

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 2
------cttgatatctattaaaaaaggtcttttgtattgttatgaatgtagg-tccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
      ||||  || | |||    |  |  ||  |    |  | |||||| | | |   | |  || | || |    |  ||||   | | |||  || ||   |||| | ||||| ||||| || ||||||||||||||||||||||| || ||  | ||  |||| |||||| |||||||||| |||| ||||||||| || || 
atctaacttgcaattttttagtttacatacttgat----tggtcaatgtaagataccctactatactttttttcatga-tatttcacaatgttgctttattg--cagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGCGAGAAATTAGTCGCAAATCTTTTCCAAATGGCTCGTGAAAATGCCCCTTCCATTATC

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 2
cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttca---tcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
 | | | | | |  |     || | || |     | |  ||    |   | | ||    ||    |   ||   || ||  ||||| | |||   |   |||| || ||||||||||||||||| || |||||||||||||||||||| ||||| || |||||||||||||| ||||| || |||||||| || || || || 
ttggttgtttttctatgtcagtttgtttttacagtgtttatacttggaaacatgt---tatagcttaagaaaagttgtttcctttttacttcccaaccttcagCGTGTCTTCATCAGACCTTGTCTCGAAGTGGATGGGTGAAAGTGAGAAGCTAGTATCAAACCTTTTCGAGATGGCCCGTGAAAGTGCTCCCTCGATTATT

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 2
---------cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
           || |     |||    |  | | |  |  | |||||    |  |    || |   | | |||   |||||       ||||  ||  |||||   |||||| ||||| |||||||| |||||||||||||||||||||||||||||| | |||||||| |||||  |||||||||| || ||||| ||||| ||||| 
aagtctgtttctgtttctggttatcgtatttttctcctccttttatgttcatgagct--taggccaataagttg--gcaagtgc---caactgctg--ttcttttgcagTGTCTCTTCTTCAGACCTGGTTTCAAAGTGGATGGGTGAAAGTGAAAAGTTAGTTTCAAATCTTTTTCAAATGGCTCGGGAGAGTGCTCCTTCCATCATC

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|208290707|gb|GE084115.1|GE084115
EST:     TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAG                         TGTTTCTTCATCAGACCTTGTTTCAAAGT
genomic: TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAGgtaaacttgt ... tcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGT
EST: gi|208146655|gb|GD947136.1|GD947136
EST:     TCATATTTAGCCAAGGCAGTTGCAACGGAAGCCGAGTCCACGTTTTTCAG                         TGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT
genomic: TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAGgtaaacttgt ... tcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT
EST: gi|21601249|gb|BQ611580.1|BQ611580
EST:     TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAG                         TGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT
genomic: TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAGgtaaacttgt ... tcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT
EST: gi|15204253|gb|BI427021.1|BI427021
EST:     TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAG                         TGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT
genomic: TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAGgtaaacttgt ... tcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT
EST: gi|193682576|gb|FK621700.1|FK621700
EST:     TCATATTTAGCCAAGGCAGTTGCAACGGAAGCCGAGTCCACGTCTTTCAG                         TGTTTCTTCATCAGACCTTGTTT
genomic: TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAGgtaaacttgt ... tcttcatcagTGTTTCTTCATCAGACCTTGTTT
EST: gi|17519421|gb|BM188463.1|BM188463
EST:     TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAG                         TGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT
genomic: TCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAGgtaaacttgt ... tcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT
EST: gi|193538431|gb|FK493761.1|FK493761
EST:     CCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAG                         TGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT
genomic: CCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTTTTTCAGgtaaacttgt ... tcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
                              ttttaac  putative branch site (score: 2)
                                            ttcttcatc  putative PPT
                            atttttaacttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA

- - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - -gaatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagcat