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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaataatatataaaatatcttgtttcaggtctcattcttcactatttcttcttaatgtcgagctaatttccaacttctatttgtttctatatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTTTCACCAGGAAAAGGAGAG

Basic information

species Glycine max
transcript GLYMA20G33580.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33580.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0073g00160.t01 (Vitis vinifera), 3'ss of exon 5
ttaataatatataaaatatcttg--tttcaggtctcattcttcactatttcttcttaatgtcgagctaatttccaacttctatttgtttctatatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTTTCACCAGGAAAAGGAGAG
  | |  | | |   |  | | |  ||| | |   | |  ||  | | |       ||  | |  |||      |      | || ||| | ||    ||||||||||||  ||||||| || ||||||||||| |||||||||||| |  ||||||| | |||   ||||
-aagtcctgtgtgggaactttaggatttgaagaaacttattttccaaatggcgaaaaactttgttcta-ccataatgagaaacttctttatctaactttcagGTATTTAATGAGTCAAAAATTGTGGAATACAGCATCAAAGAAAATCTAATTTCACCTGAAAAGACAGAG
















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|298185401|gb|HO030614.1|HO030614
EST:     GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAG                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
EST: gi|192302699|gb|FG993719.1|FG993719
EST:     GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAG                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
EST: gi|120491293|gb|EH219460.1|EH219460
EST:     GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAG                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
EST: gi|192302698|gb|FG993718.1|FG993718
EST:     GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAG                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
EST: gi|192302196|gb|FG997276.1|FG997276
EST:     ATACTCTTCCCAAG                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: ATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
EST: gi|8827104|gb|BE210834.1|BE210834
EST:     GGTGAAACAGATCAAATCAGCAGTGCTAT-CTCTTCC-A-G                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: GGTGAAACAGATCAAATCAGCATT-CTATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
EST: gi|298163106|gb|HO011839.1|HO011839
EST:     GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAG                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
EST: gi|120491336|gb|EH219503.1|EH219503
EST:     GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAG                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
EST: gi|151400704|gb|EV270518.1|EV270518
EST:     GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAG                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
EST: gi|192302195|gb|FG997275.1|FG997275
EST:     GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAG                         GTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT
genomic: GGTGAAACAGATCAAATCAGCATTCTATACTCTTCCCAAGgttttgatta ... tatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttcttaatgtcgagctaatttccaacttctatttgtttctatatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTTTCACCAGGAAAAGGAGAG
                agctaat  putative branch site (score: 3)
                                       tttctat  putative PPT
                                 tatttgtttctatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaataatatataaaatatcttgtttcaggtctcattcttcactatttcttcttaatgtcgagctaatttccaacttctatttgtttctatatacctcagGTATTTAAGAAGTCAAAGATAGTGGAATACAGTATCAAAGAAAATATGGTTTCACCAGGAAAAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - ataaaata
- - - - - - - - - - - - - - - -ctcattc