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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacagaatgcacaacgactgttgtactttgctcgtatattttactagatggcaatagtgcatcattccgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAA

Basic information

species Glycine max
transcript GLYMA13G17370.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G17370.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g01930.1 (Oryza sativa), 3'ss of exon 4
agacagaatgcacaacgactgttgtactttgctcgtatattttactagatggcaatagtgcatca-ttccgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAA
      || |  |  |  ||   ||  ||  ||| ||     ||   |     || |    || | ||   ||  | |     |          |   |||||| |||||||| ||| |  | ||||||||    ||| ||   ||||  ||||||||||||||||| || |||||||||||||||||||||||||| |||
-ctttaaaggggcttctccttcagtttttccctcctaggaaatagctgtccaaaacaaccgattaatttttctaatgagcaaatttctttgtgctgcacagGATCTCTGTAACATTTGTGAACAAGGATGGCACAGAGCAGACAATCAGTGTCCCTGTTGGAATGTCCATCTTAGAAGCTGCTCATGAAAATGACATCGAA

upper sequence: GLYMA13G17370.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g26650.1 (Oryza sativa), 3'ss of exon 3
----agacagaatgcacaacgactgttgtactttgctcgtatattttactagatggcaatagtgcatcattccgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAA
       | |   || ||       || |  ||     ||  || ||  |  ||  | | | |      ||      |  |  || | |   ||   | |||||||||||||| |||||| ||||||||||||| ||||| |||| | | ||||| ||| | |||||||| ||| |||| || || ||||| |||||||| |||
tttttatctgttggctcatgtgtgattttggttataaagtccatgttgttttatt-ctacaatttgaacttgaatatcaaatattataatttaa---tttgcagGATATCTGTGACTTTTGTTGATAAGGATGGCGAGGAAAAGCTTGTTAAAGTACCTATAGGAATGTCAATGCTAGAGGCAGCACATGAGAATGACATAGAA

upper sequence: GLYMA13G17370.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G013607_T02 (Zea mays), 3'ss of exon 4
agacagaatgcacaacgactgttgtactttgctcgtatattttactagatggcaatagtgc-atcattccgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAA
||    | || |     | |||||  ||||       |||||         ||| |  |   || |||       ||| ||||      |   | |  ||| || || ||||| ||| |  | ||||||||    || |||   ||    || || ||||||||||| ||||||||||||||||||||||| ||||| || 
agttttactgaattgttagtgttgagctttcaataattatttagggtagaagcagtcctctgatgattgttgaggttatttttctccatactgtga-acagAATCTCGGTAACATTTGTCAACAAGGATGGCTCAGAAAAGACAATATGTGTTCCAGTTGGAATGTCCATGTTAGAAGCTGCTCATGAAAACGACATAGAG

upper sequence: GLYMA13G17370.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
--agacagaatgcacaacgactgttgtac-tttgctcgtatatt-ttactagatggcaatagtgcatcattccgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAA
  |       | |||| | |  ||| ||| ||| ||| ||  |  || ||  |||   ||    | |  |    || || | |  |  |   ||  || ||||||||||||||  | ||| ||||||||||||| |||||  | || || |  |||||  ||||||||||||||||||||||||||||||||||||| || |||
caatcttagttacacatc-atggttctacatttcctcttaactcatttctgcatgtagattac-cctggtgtttcttctcattcatatatttaa--ttgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA

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|254329164|gb|GR833536.1|GR833536
EST:     ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAAC                         GATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT
genomic: ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAACgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT
EST: gi|193427054|gb|FK397515.1|FK397515
EST:     ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAAC                         GATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT
genomic: ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAACgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT
EST: gi|193346230|gb|FK309722.1|FK309722
EST:     ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAAC                         GATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT
genomic: ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAACgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT
EST: gi|14125826|gb|BG790264.1|BG790264
EST:     ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAAC                         GATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT
genomic: ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAACgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT
EST: gi|254329165|gb|GR833537.1|GR833537
EST:     ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAAC                         GATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT
genomic: ACAATGACTACTAACAACACTACTGAGGAAGGAAGTGAACAAGAACAAACgtaagttctt ... cattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatggcaatagtgcatcattccgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAA
                          tccttac  putative branch site (score: 2)
                             ttacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacagaatgcacaacgactgttgtactttgctcgtatattttactagatggcaatagtgcatcattccgctccttactttttgaggcaacattatgcagGATATCTGTAACTTTTATTGATAAGGATGGTGAGGAGAAGCATATCAAAGTCCCTGTTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGACATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - -gaatgca
- - - - - - - - -actgttg