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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtttttgtatttgaatcagttgtcacttcttgtgttcagttgatatgattagatgcaggaaatgtaatgcttctcattatgtcttgttctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG

Basic information

species Glycine max
transcript GLYMA03G32800.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 1
attgtttttg-tatttgaatcagttgtcacttcttgtgttcagttgatatgattagatgcaggaaatgtaatgcttctcattatgtcttgttctttact-agGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
 || |      || |||  ||   | | |    |  | ||  | |  | |  |||  ||   ||| | |  |    |  |   ||     |  |||  | ||||||||||||| |||||  || | |||||||| ||||| || ||||| ||||| ||||| || |||||||| |||||||| || ||||| || || ||||
cttataaccaatagttggctctactattaaacttgctcttatgctctttt--ttacttgtgagaagttttttataaccaaacttgataaatcatttcttcagGTTCTCTCTGTGGTTGGAATTTTGCAAGATGAGGTTGACCCTATGGTTTCTGTCATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCGGACATCGGTG

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 1
-attgtttttgtat--ttgaatcagttgtcacttcttgtgttcagttgatatgattagatgcaggaaatgtaatgctt-ctcattatgtcttgttctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
 ||  ||||  |||  | |||| |||        | |   | ||  ||   |  | |  |  | |   |   | |||| |||| ||  ||    | |   | ||||||| ||||| || ||  || | ||||||||||||||||| ||||| ||||| ||||| || || || || ||  ||||||| |||||||| |||||||
tatcattttcttatgatcgaataagtgactcaaccgtacatccatgtggc-tagtaattttaatgctctagcaagcttgctcactaaatccctattt---ccagGTTCTGTCTGTGGTCGGAATTTTGCAAGATGAAGTTGATCCTATGGTTTCTGTGATGAAAGTGGAGAAAGCTCCGCTGGAATCCTATGCTGACATTGGTG

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 1
attgtttttgtatttgaatcagttgtcacttcttgtgttcagttgatatgattagatg--caggaaatgtaatgcttctcattatgtcttgttctttact--agGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
  |||  |   ||    ||  ||||| | ||      || ||| ||| || || ||    ||||| | ||    ||| |             | || |||  ||||||||||||| |||||  |  | ||||||||||||||||| ||||| ||||| ||||| || || || || ||||||||||| |||||||| |||||||
--tgtgctca-ataaccatttgttgtaaattgcacgctttagtggat-tgttttgaccatcaggagaggttcatcttgtttgctcactcaaatgttcacttcagGTTCTCTCTGTGGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCGCCTTTGGAATCTTATGCTGACATTGGTG

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 1
---attgtttttg-tatttgaatcagttgtcacttcttgtgttcagttgatatgattagatgcaggaaatgtaatgcttctcattatgtcttgttctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
   ||   |  || |  |  | | |  |      | || | |  | ||  |    ||  ||||       ||||      |    |  | ||   |||    ||||||| || || |||||  || | ||||| ||||||||||| ||||| ||||| ||||| || |||||||| |||||||| || |||||||| |||||||
aaaatcaatgctgctcctcaagtgatgtactctgtgttttatgtacttccttgatttgaatgcttatttagtaaacagcttggccaaatgtttccctt----agGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCTGTGATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCTGACATTGGTG

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 1
attgttt--ttgtatttgaatcagttgtcacttcttgtgttcagttgatatgattagatgcaggaaatgtaatgcttctcattatgtcttgttc-tttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
 |||||   ||| |  || || ||| |  ||   ||       || |     |  |    |||    | |  |   ||  |   |    ||||   |    ||||||| ||||| |||||  |  | ||||||||||||||||| ||||| ||||| ||||| || || || || ||||||||||| |||||||| |||||||
tttgttgcattgcacatgcattagtgg--accgtttacaactggtaggggatagcaagc-cagcttgttttctcactcaaacagtcaaatgtttactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCACCTTTGGAATCTTATGCTGACATTGGTG

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
attgtttttgtatttgaatcagttgtcacttcttgtgttca-gttgatatgattagatgcaggaaatgtaatgcttctcattatgtcttgttctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
         |||||    |      |    |    ||   | |||||    |||           |||| ||  || | |||||      || | |  ||||| ||||||||||||||| |||||||||||||||| ||||||||||| ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| |
---------gtattgagttttacaatgctcttccatggaaacgttgaaccaattcttct------atgtgatattttttattat------ttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 1
attgtttttgtatttgaa-tcagttgtcacttcttgtgttcagttgatatgattagatgcaggaaatgtaatgcttctca---ttatgtcttgttctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
         |||| |||| | ||   | |    |  ||||   ||| | ||||||       |   |||  ||  | |     |  ||  ||||| | |  ||||||||||||||||||||| |||| ||||||||||| ||||||||||| ||||| ||||| || || || || |||||||| ||||||||||||||||| |
---------gtatgtgaaattagggtttaagaatcttgttt--ttgttgtgattacgattgtgtgttgttgtggatttagggttgctgatttgttttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTTGAGAAAGCTCCTTTGGAGTCATATGCTGATATTGGAG

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 1
attgtttttgtatttgaatcagttgtcacttcttgtgttcagttgatatgattagatgcaggaaatgtaatgcttctcattatgtcttgttct---ttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
 |   |||| || ||  ||   || | | |     ||   |  |  |    | |    ||     |     | |||| ||  |   |||| ||   |    ||||||| ||||||||||| ||||| ||||| ||||||||||||||||| || || ||||| || || ||||| || ||||||||||||||||| || || |
-tctgttttatagtt--atgcattcttattcacattgaagatgtagttccttcaccatcatagtttcaggaggttcttatattactttgtgctgtctcgtcagGTTCTTTCTGTTGTTGGTCTTCTCCAAGACGAAGTTGATCCAATGGTGTCCGTAATGAAAGTTGAGAAGGCTCCATTGGAATCATATGCTGACATAGGAG

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 1
attgtttttgtatttgaatcagttgtcact-tcttgtgttcagtt---gatatgattagatgcaggaaatgtaatgcttctcattatgtcttgttctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
   |||   |||  ||| | |||  |  |  ||  |      |||   | ||| |  ||||   || ||  |  | |     ||| |   ||||  | | | |||| || || ||||| ||  | || |||||||| || || |||||||| ||||||||||| || ||||| || ||| | || ||||||||||| |||||||
-aagttagagtaactga-ttagtcctggcggtcacgaacatggtttgagttatcaccagatcatgggaaacttgtccaaacgatt-ttctttgtcttgtgc-agGTCCTTTCAGTTGTGGGATTGCTGCAAGATGACGTGGACCCAATGGTTTCTGTTATGAAAGTTGAAAAAGCTCCTCTAGAGTCATATGCTGACATTGGTG

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|13789045|gb|BG651636.1|BG651636
EST:     TTGATAAGGATCAGCTCGAACCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGCTCGAACCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|6725713|gb|AW310112.1|AW310112
EST:     TTGATAAGGATCAGCTCGAACCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGCTCGAACCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|151412684|gb|EV282496.1|EV282496
EST:     TTGATAAGGATCAGCTCGAACCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAAATGAAGTTGATCCAATGGTCTCT
genomic: TTGATAAGGATCAGCTCGAACCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgattagatgcaggaaatgtaatgcttctcattatgtcttgttctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG
 agttgat  putative branch site (score: 5)
                                       tcttgttctttact  putative PPT
                 aaatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtttttgtatttgaatcagttgtcacttcttgtgttcagttgatatgattagatgcaggaaatgtaatgcttctcattatgtcttgttctttactagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTCGAAAAGGCCCCTTTGGAATCATATGCTGATATTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - -tgtcact
- - - - - - - - - - - - - - - - -tgtgttc
- - - - - - - - - - - - - - - - - - - - - -tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcttg