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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagtctcatttaccgattaagtcttgtgttctggaaattttcttgacattgcttaatcatttttggcttttaactgacttgaatgctcttttgtttcttttttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATGAAAGTTGGGAATTCTATCCGCAGCTGTGGTTATGGAGAA

Basic information

species Glycine max
transcript GLYMA01G43470.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43470.5 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 2
gtgaagtct-catttaccgattaagtcttgtgttctggaaattttcttgacattgcttaatcatttttggcttttaactgacttgaatgctcttttgtttcttttttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATGAAAGTTGGGAATTCTATCCGCAGCTGTGGTTATGGAGAA
     || |    |||  | || |  ||  |  ||   ||  | |     || |   ||||   |||||  ||| | || |      | |  | ||||||||| |||      || | || || ||   ||||||||| || ||||||||||||||| | |||||||||||||| ||||| |||||||| ||||||  |   |||
-----gtatatggttattgttttatgctatttctccataaggtct----gcaatttataatttgttttgattttcagctaa--aagttacattgttgtttcttcttt----gcagGCTGGTAAATATGTGTGGCTAACTTATAAAGAAGTATATGACAAAGTGATGAAAGTTGGAAATTCCATCCGCAGTTGTGGTGTTAATGAA
















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|213596837|gb|DB964100.1|DB964100
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|208183242|gb|GD981464.1|GD981464
EST:     AATATCCATCAAATCCAATACTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|209718138|gb|BW657797.1|BW657797
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|213593798|gb|DB957918.1|DB957918
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|213603942|gb|DB964962.1|DB964962
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|209713723|gb|BW681863.1|BW681863
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|193373262|gb|FK336142.1|FK336142
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|213617043|gb|DB961523.1|DB961523
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|209712293|gb|BW668487.1|BW668487
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|209718875|gb|BW669062.1|BW669062
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
EST: gi|16996081|gb|BM085453.1|BM085453
EST:     AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAG                         CCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG
genomic: AATATCCATCAAATCCAATGCTTGGTCGCCGGGAAATTGTGGATGGGAAGgtgaagtctc ... ttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttttggcttttaactgacttgaatgctcttttgtttcttttttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATGAAAGTTGGGAATTCTATCCGCAGCTGTGGTTATGGAGAA
               aactgac  putative branch site (score: 2)
                           tgctcttttgtttctt  putative PPT
                                ttttgtttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagtctcatttaccgattaagtcttgtgttctggaaattttcttgacattgcttaatcatttttggcttttaactgacttgaatgctcttttgtttcttttttctgcatagCCGGGCAAGTACAAGTGGCTAACATACAAAGAAGTATATGACCAGGTGATGAAAGTTGGGAATTCTATCCGCAGCTGTGGTTATGGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA