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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttcaacgactctagggttgtttattttttttttctgaactgaaattcgatgattgtggtcactgtaactgacggctcctatgaattttttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAGAAGCAGATGAGGCTCGCCGGTGACGTGGCAGGTACCAGAAAGGCGGCTA

Basic information

species Glycine max
transcript GLYMA05G32030.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 1
------------------------------------------------------------------ccttcaacgactctagggttgtttattttttttttctgaactgaaattcgatgattgtggtcactgtaactgacggctccta---tgaattttttatttgtagGCAAATACGGGA-------------AATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAGAAGCAGATGAGGCTCGCCGGTGACGTGGCAGGTACCAGAAAGGCGGCTA
                                                                      |  |  | |    |  |       || |  |||    |    ||||||   | | |    |  | |||| | ||   |   |||   | ||  |||| | |  || | |||             ||  | || ||||||||||||    | || ||||||||||||||||||||||| ||||| || || || || || || ||||| |   
gtgagctcacctccctcctcccctcccccaccccgaccctccgcccgcctctccggggttttggccttcccgcccgccccgccgcggcccgcacttctcatctagggt----ttcgat--ctcttgcgggttgatctgatgccttgcaatctgaccctgtttcttgtggaccgatgcagGAGGGTAACAGTACCAACCTCGATGCGGCGATAGAGTCGCTCCTCAACGTGGAGAAGCAGATGAGGCTGGCCGGCGATGTCGCCGGCACGAGGAAGGCCG---

upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------ccttcaacgact--ctagggttgttt---attttttttttctgaactgaaattcgatgattgtggtcactgtaactgacggctccta---tgaattttttatttgtagGCAAATACGGGA-------------AATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAGAAGCAGATGAGGCTCGCCGGTGACGTGGCAGGTACCAGAAAGGCGGCTA
                                                                                   |   ||| ||  |  | |  |      |        | | |  ||    ||      | | |   | |  | |||    |||      ||| | |  | ||  | | | | | | |||             ||  | |||||||| ||||||    | |||||||||||||||||||||||||| ||||| || || || || ||  | ||||| |   
gtgagccctccgccggcctctagcgccaccttgttctccatccacatctcgcgcctccgcgcttcaccccatttcctagtgtttgtgacggctggccggtgcaggccgcgaccgcgccctcccggcctagggtttcgatctcgcgccgatt-catctgctacctcgcggtttgactctgctcttgcttgacgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTGGAGAAGCAGATGAGGCTGGCCGGCGATGTCGCCGGCACGCGGAAGGCCG---
















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|37996134|gb|CF807723.1|CF807723
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|19271260|gb|BM887516.1|BM887516
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|18039945|gb|BM308239.1|BM308239
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|24206051|gb|BU965304.1|BU965304
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|26047818|gb|CA784480.1|CA784480
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|37997022|gb|CF808611.1|CF808611
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|17519815|gb|BM188857.1|BM188857
EST:     CCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: CCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|7925406|gb|AW831371.1|AW831371
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|23731285|gb|BU763760.1|BU763760
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|192295223|gb|FG986942.1|FG986942
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
EST: gi|192309222|gb|FG999449.1|FG999449
EST:     AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATG                         GCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG
genomic: AATTTCACGACTCCTTCGGAGATCTCTCTCTCGCCCATAATCCAACCATGgtaccctctc ... ttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgatgattgtggtcactgtaactgacggctcctatgaattttttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAGAAGCAGATGAGGCTCGCCGGTGACGTGGCAGGTACCAGAAAGGCGGCTA
                      aactgac  putative branch site (score: 2)
                                         ttttttattt  putative PPT
                                   tatgaattttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttcaacgactctagggttgtttattttttttttctgaactgaaattcgatgattgtggtcactgtaactgacggctcctatgaattttttatttgtagGCAAATACGGGAAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAGAAGCAGATGAGGCTCGCCGGTGACGTGGCAGGTACCAGAAAGGCGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
ccttcaa
- - - - - - - -gggttgt
- - - - - - - - - - - - - - - - - tctgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - gattgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgta