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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattggtgcatttggtaggtccacgtttgtatgcaatgtgtctcgattgattttgtttcgtacatttgtgtatctggattaatcaactcttctctctcagGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATTGCTAGGAGAACCCCTGGATTCACTGGGGCTGATCTGCAGAATTTGATGA

Basic information

species Glycine max
transcript GLYMA06G02200.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 1
gattggtgcat-ttggtaggtccacgtttgtatgcaatgtgtctcgattgattttgtttcgtacatttgtgtatctggattaatca-actcttctctctcagGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATTGCTAGGAGAACCCCTGGATTCACTGGGGCTGATCTGCAGAATTTGATGA
  ||  || ||  || | |        || |  ||        | |||    |||  |  ||||    | | |  |  |  |  ||   | || |||   |||| || || |||||||| || || ||||| ||||| || ||||| ||||||||  ||||||||||||| |||||||| |||||||| || || |||||||
-ctttctgaatgctgatcgacttttccttatg-gcttcccaatttgataagcttttatctgtaccaaagcgcaagtttacaagacatgttattgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATTGCCCGGAGAACCCCTGGTTTCACTGGAGCTGATCTTCAAAACTTGATGA

upper sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G126361_T01 (Zea mays), 3'ss of exon 1
gattggtgcatttggtaggtccacgtttgtatgcaatgtgtctcgattgattttgtttcgtacatttgtgtatctggattaatcaactcttctctctca----gGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATTGCTAGGAGAACCCCTGGATTCACTGGGGCTGATCTGCAGAATTTGATGA
 |       ||||   |     | |||||  |       || ||   ||||||  |||   |  | ||| ||  ||   | |  |    || | | |||    ||| || ||  ||||||| ||  | || || |||||||||||||| ||||||||||| || |||||||| |||||||| ||||| || || ||  | ||||
cacaatattatttaaaaaag--aagtttgatttttcccagtatc--ctgatttcattttaaatgtatgtatacatgagcttacaagtctttttttatcaaatagGTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATTGCTAGAAGGACCCCTGGTTTCACTGGTGCTGACCTCCAAAACCTCATGA

upper sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 1
gattggtgcatttggtaggtccacgtttgtatgcaatgtgtctcgattgattttgtttcgtacatttgtgtatctggattaatcaactcttctctctcagGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATTGCTAGGAGAACCCCTGGATTCACTGGGGCTGATCTGCAGAATTTGATGA
       |  | |  | | |     ||| | |  |  |||   | || ||    || | ||  ||     | | ||| |||             |  |||||||||||||||||||||||  |||  |||||||||||||  |||||| |||| |||||||| || || |||||||| |||||| |||||||  ||||||
-------gtttcttcttgctttcattttctgt-tagagtgaaacaatggagacagtgtggtgaataatgttgtgtggttta-------------ttgcagGTGCATTCTAGAGGAAAAGCTATTGGGAAGGATGTTGATTACGAAAAAGTTGCGAGGAGAACTCCGGGTTTCACTGGTGCTGATTTGCAGAACCTGATGA

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|193535975|gb|FK491301.1|FK491301
EST:     AAGTTACTGTGGATAGACCTGATGTTGCCGGCAGAGTTAAAATCCTTCAG                         GTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAA
genomic: AAGTTACTGTGGATAGACCTGATGTTGCCGGCAGAGTTAAAATCCTTCAGgtgagtctgt ... tctctctcagGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAA
EST: gi|208216597|gb|GE013425.1|GE013425
EST:     AAGTTACTGTGGATAGACCTGATGTTGCCGGCAGAGTTAAAATCCTTCAG                         GTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATT
genomic: AAGTTACTGTGGATAGACCTGATGTTGCCGGCAGAGTTAAAATCCTTCAGgtgagtctgt ... tctctctcagGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgattttgtttcgtacatttgtgtatctggattaatcaactcttctctctcagGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATTGCTAGGAGAACCCCTGGATTCACTGGGGCTGATCTGCAGAATTTGATGA
                               gattaat  putative branch site (score: 3)
                                     tcaactcttctctctc  CT-rich tract
                                attaatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattggtgcatttggtaggtccacgtttgtatgcaatgtgtctcgattgattttgtttcgtacatttgtgtatctggattaatcaactcttctctctcagGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATTGCTAGGAGAACCCCTGGATTCACTGGGGCTGATCTGCAGAATTTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - tgcattt
- - - - - - - - - - - - - - gtatgca
- - - - - - - - - - - - - - - - - - -gtgtctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caactct