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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggtctactttcatactatcttctgaatctattaaagtatttttccttctacacaatttttgtagtcatatcatggtaactaggtttacatttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG

Basic information

species Glycine max
transcript GLYMA12G08670.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g57670.1 (Oryza sativa), 3'ss of exon 3
-taggtctactttcatactatcttctgaatctattaaagtatttttccttctacacaatttt--tgtagtcatatcatggtaactaggtttacatttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG
  | |  |  || | ||| |   ||    || || | |||||     |||  |  || | ||    || || || | || | |  |  |||    ||  ||||||||||||||||||||| |||||||| |   ||||||||||| ||||||| ||||| |||   ||||||||||| ||||||||||| || ||||| ||
gcatgatttgttcc-taccaatatcattttccataagagtataagaactttcatccagtgttagcataatcttaccctgttgagca--tttgtgcttgagtagGTAAAAGAAGAGGCACAGCAACTTGCCCGTGTTTTTGAAACTATTGGGGCATTCAAAGTGCCACGTAAAGGTGGGAAAGGAAAACAGATATTTGGGAG

upper sequence: GLYMA12G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G096962_T01 (Zea mays), 3'ss of exon 3
---taggtct--actttcatactatcttctgaatctattaaagtatttttccttctacacaatttttgtagtcatatcatggtaactaggtttacatttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG
   || |||   |   | |||   || |   | ||||| || | ||||||     |        ||| || | ||  | |  |||  ||   |  ||||   |||||||||||||| || ||||||||||||| | ||||||||||  |||| ||||||||  |    || |||||||| ||||||||||| || ||||| ||
atttaagtcctaagcatgatatgttcatgaaattctatcaatgcatttttatcagtttttg---tttataattatggcct--taagaagtcctctatttacatagGTAAAAGAAGACGCGCAACAACTTGCTCGAGTTTTTGAAACCATTGGCGCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAG

upper sequence: GLYMA12G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0061g00770.t01 (Vitis vinifera), 3'ss of exon 3
--taggtctactttcatactatcttctgaatctattaaagtatttttccttctacacaatttttgtagtcatatcatggtaactaggtttacatttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG
  |   |  |    | || | | | || |   ||     ||| | |      |   |   |||  ||    |  | || |   ||  ||  | |  ||| |||||||||||||||| |||||| | |||||||| |||||||||||||| |||||||||||||| || |||||||| |||||||| ||||| ||||||||
agtttatggatgcacttattttttcctcaccataaatgtgtactgtcataaatttccctatttgataaatttgacttgtttcttatatt--cttccctgcagGTAAAAGAAGAGGCCCAACAAATGGCTCTAATGTTTGAAACTGTTGGAGCTTTCAAGGTGAAACGCAAAGGTGGAAAAGGAAAGCAAATCTTTGGAAG

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|11687696|gb|BF595372.1|BF595372
EST:     GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGG                         GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCT
genomic: GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGGgtaatttttc ... atttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCT
EST: gi|23063991|gb|BU578764.1|BU578764
EST:     GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGG                         GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCT
genomic: GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGGgtaatttttc ... atttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCT
EST: gi|151399558|gb|EV269429.1|EV269429
EST:     GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGG                         GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCT
genomic: GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGGgtaatttttc ... atttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCT
EST: gi|13181262|gb|BG352602.1|BG352602
EST:     GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGG                         GTAAAAGAAGAGGCACAACAAACTTGCTCTAATTTTTGAAACTGTTGGGGC
genomic: GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGGgtaatttttc ... atttctgtagGTAAAAGAAGAGGCACAACAA-CTTGCTCTAATTTTTGAAACTGTTGGGGC
EST: gi|7796407|gb|AW781804.1|AW781804
EST:     GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGG                         GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCT
genomic: GGAAATGAAGATAGAAGAGGAAAGAATTGAGGCTGAGAAAAGACGGgtaatttttc ... atttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttctacacaatttttgtagtcatatcatggtaactaggtttacatttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG
                             tggtaac  putative branch site (score: 2)
                                            catttct  putative PPT
          aatttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggtctactttcatactatcttctgaatctattaaagtatttttccttctacacaatttttgtagtcatatcatggtaactaggtttacatttctgtagGTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - -tcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatca