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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actctatcttccatttctctattcttattctgtgtaccttgatggcctgttgttattacccgcaattcaaatagattctatgtgtgctatgcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATCTTGCACGATGGTTCAATTCAATAGTGGAAGAACATGGTACTGCCTTAAA

Basic information

species Glycine max
transcript GLYMA20G22170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G22170.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g16520.1 (Oryza sativa), 3'ss of exon 4
actctatcttccatttctctattcttattctgtgtaccttgatggcctgttgttattacccgcaattcaaatagattctatgtgtgctatgcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATCTTGCACGATGGTTCAATTCAATAGTGGAAGAACATGGTACTGCCTTAAA
            | || |||  | |  ||   | ||   | ||    | |  || |        ||   | |   ||    |||        || |  |||  | ||  |  |||||||||||||||||| ||| |||||||||| ||| ||||  || ||||||||    ||||  ||  |    |  ||        |
----------gtaattgtctggtttcttt---tataatct-atattttatcattctatatgtttatattacttactttggagtggcacccctttatttagGGACAGGCCAACGATGGGAAAGTCTAAGGAGGTCCAAGAAATATCAAAACCTTGTTCGCTGGTTCAACAGCATAGCAGACTATTCAGACACACTAGATGA

upper sequence: GLYMA20G22170.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G057491_T01 (Zea mays), 3'ss of exon 4
actctatcttccatttctctattcttattctgtgtaccttgatggcctgttgttattacccgcaattcaaatagattctatgtgtgctatgcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATCTTGCACGATGGTTCAATTCAATAGTGGAAGAACATGGTACTGCCTTAAA
     | ||     ||| | |||||| ||    |     ||   ||   |||||||        ||| |     || ||  ||    | | |||   ||||   |||  |  ||||||| ||||||||||| ||||||||||| | ||||||||  || ||||||||    ||||    |||| |  ||    |  | ||
--gtaagctgtgtgttcaccattcttctttcaggcgggctgtgtgc--attgttat--------atttagc---atgctgcgtcatttttcctt---cagGAATTGGTCAACGATGGGAGAGTCTAAGGAAATCAAAGAAATACCAAAATCTTGTCCGCTGGTTCAACAGCATAGATTCAGAATACAGTGACACACTGAA

upper sequence: GLYMA20G22170.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G046932_T01 (Zea mays), 3'ss of exon 4
actctatcttccatttctctattcttattctgtgtacc-ttgatggcctgttgttattacccgcaattcaaatagattctatgtgtgctatgcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATCTTGCACGATGGTTCAATTCAATAGTGGAAGAACATGGTACTGCCTTAAA
                 |    | |     |||  ||| ||  |       | |   |    ||||| |||       ||   ||    ||  || |  |||   |||  || | ||||| ||||||||||| ||||||||||| | ||||||||  || ||||||||    ||||    |||| |       ||  | ||
----------------gtaagctgtgggattgttcaccattcttatttcagtctggctctaggcaatgcaatgtttaacttgctgcatcatttttctttagGAATTGGTCAGCGGTGGGAGAGTCTAAGGAAATCAAAGAAATACCAAAATCTTGTTCGCTGGTTCAACAGCATAGATTCAGAATACAAAGAGGCACTGAA

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|193470509|gb|FK437738.1|FK437738
EST:     TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAG                         GTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
genomic: TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAGgtaaaggctt ... gcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
EST: gi|254338304|gb|GR849829.1|GR849829
EST:     TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAG                         GTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
genomic: TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAGgtaaaggctt ... gcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
EST: gi|209725493|gb|BW677790.1|BW677790
EST:     TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAG                         GTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
genomic: TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAGgtaaaggctt ... gcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
EST: gi|213589731|gb|DB965863.1|DB965863
EST:     TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAG                         GTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATA
genomic: TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAGgtaaaggctt ... gcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATA
EST: gi|213588339|gb|DB967825.1|DB967825
EST:     TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAG                         GTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
genomic: TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAGgtaaaggctt ... gcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
EST: gi|213607818|gb|DB959129.1|DB959129
EST:     TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAG                         GTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
genomic: TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAGgtaaaggctt ... gcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
EST: gi|51345223|gb|CO985956.1|CO985956
EST:     TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAG                         GTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
genomic: TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAGgtaaaggctt ... gcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
EST: gi|209720614|gb|BW677322.1|BW677322
EST:     TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAG                         GTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC
genomic: TGGTTATTCATTGTCAATTGCAGACCTAGCAATCTGGGCAGGTCTTGCAGgtaaaggctt ... gcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttgttattacccgcaattcaaatagattctatgtgtgctatgcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATCTTGCACGATGGTTCAATTCAATAGTGGAAGAACATGGTACTGCCTTAAA
                                            tgctttt  CT-rich tract
                  aattcaaatagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actctatcttccatttctctattcttattctgtgtaccttgatggcctgttgttattacccgcaattcaaatagattctatgtgtgctatgcttttgcagGTTCTGGAAAGAGATGGGAAAGTCTAAGGAAGTCAAAGAAATATCCAAATCTTGCACGATGGTTCAATTCAATAGTGGAAGAACATGGTACTGCCTTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - ccatttc
- - - - - - - - - - - - - - - tgtgtac
- - - - - - - - - - - - - - - - - - - -tgatggc
- - - - - - - - - - - - - - - - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -acccgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtgc