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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatgttgtgtacaagttatctcttttgatgcagactgttttctgtctgattgttaagataatactgatttaaggaagtgatttttttcatgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA

Basic information

species Glycine max
transcript GLYMA13G29010.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
cttatgttgtgtacaagttatctcttttgatgcagactgttttctg----tctgattgttaagataatactgatttaaggaa-gtgatttttttcatgtgaa-cagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
      | |    | | | | |   || | || ||| || |    |    | |||   | |    |    ||||| ||  |   || |||| ||    |||| ||||| |||||||||||||| |||||||| |||||||||||||| |||||||| || || |||||||| || ||| | ||||| |||||||| || |||||||
------tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcatagaagatttgattgaaaaaccatgtttttgttttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA

upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
-------------------------------------------------------------------------------cttatgttgtgtacaagttatctcttttgatgcagactgttttctgtctgattgttaagataatactgatttaagga----agtgatttttttcatgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                                                                                |||| || |   |      |   | |       |  | |||  | |||   |  |||     |  |  |||   ||    | ||| |  ||  || |   ||||| ||||||||||| |||||||||||  ||||||| || || || |||||||| ||| ||||||||||||| || |||||   |||||||||||||||||
gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaat-tttgcagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA

upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S70_181V6.1 (Physcomitrella patens), 3'ss of exon 15
-----------------------cttatgttgtgtacaagttatctcttttgatgcagactgttttctgtctgattgttaagataatactg-atttaaggaagtgattttttt--------catgtga---------acagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                        ||||   |  |    | |     | |  | |    |  |  | |||     |||||    ||| ||| |||| | |   |  |||| ||        |||||||          ||||| ||||||||||| ||||||||||||||||||||||| ||||| ||| |||||||  ||||||| || || || |||||   ||| ||||| || ||||
gtgaatatttcatacctcgaattattatccagaatttcggattcacttctgcaagtcatcgatgatgtgtagtgctgttattgaaattctgtatttcaagtgttttttttgttgttaaacgcatgtgatgttaaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTGATTGACCGGGAGTACCTTGAAAGGGACAAAGCCAATCCTCAGATCTACA

upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S143_152V6.1 (Physcomitrella patens), 3'ss of exon 15
--------------------cttatgttgtgtacaagttatctcttttg---atgcagactgttttctgtctgattgttaagataatactgatttaaggaagt---------gatttttttcatgtga----acagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                     ||||| | |  |    ||   |   |||   |   | |   |  | |   | || | |  || ||| | ||||| |  || |          |    |||  ||| |     ||||||||||||||||| ||||||| ||| |||||||| || ||||| || ||||||||  |||||||||| || || |||||   ||| ||||| || ||||
gtgaggatttcattcctggaattatgatttagaatctttggtttacttgtgcaaataaatgataatgtaaataatcgctgtgaaaatgccgatttcaaaaactttgtcgtccaacgcatttgttgttacttcgcagCTCAAATTTCCAATCAAACCAGTTGATTTGAAGAAGAGAATCGAGAGTCTGATTGACCGGGAGTATCTTGAAAGGGACAAAGCCAATCCTCAGATTTACA

upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ14633 (Selaginella moellendorffii), 3'ss of exon 16
cttatgttgtgtacaagttatctcttttgatgcagactgttttctgtctgattgttaagataatactgatttaaggaagtgatttttttcatgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                              |   | |||  | ||||  || |||   |   |  ||| | || |       ||||||   ||||| |||||||| || || ||||| ||||| |||||||||||| | ||||| |||||||| ||  | |||||  ||||| |||||||||||||||||||  ||||||
-----------------------------gtaaggcctggctgctgttggaatgtggtgccgacgctg-tatatg-------ttttttgtgtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTGATCGACCGCGAGTACTTGGAGCGAGACAAGAACAACCCTCAGGTATACA

upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ26297 (Selaginella moellendorffii), 3'ss of exon 16
cttatgttgtgtacaagttatctcttttgatgcagactgttttctgtctgattgttaagataatactgatttaaggaagtgatttttttcatgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                              |   | |||  | ||||  || |||   |   |  |||       ||  || ||||||   ||||| |||||||| || || ||||| ||||| |||||||||||| | ||||| |||||||| ||  | |||||  ||||| |||||||||||||||||||  ||||||
-----------------------------gtaaggcctggctgctgttggaatgtggtgccgacgctg-------gatatg-ttttttgtgtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTGATCGACCGCGAGTACTTGGAGCGAGACAAGAACAACCCTCAGGTATACA

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|58018820|gb|CX705562.1|CX705562
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... atgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|193358058|gb|FK322696.1|FK322696
EST:     AACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: AACTCTTCCAACAGgtgacattat ... atgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|208178526|gb|GD977485.1|GD977485
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... atgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|9258851|gb|BE346998.1|BE346998
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... atgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|58019102|gb|CX705844.1|CX705844
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... atgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|19345773|gb|BM890653.1|BM890653
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... atgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
EST: gi|16344141|gb|BI969736.1|BI969736
EST:     CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG                         CTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG
genomic: CTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAGgtgacattat ... atgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgattgttaagataatactgatttaaggaagtgatttttttcatgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA
                  tactgat  putative branch site (score: 2)
                                     tttttttcat  putative PPT
     attgttaagataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatgttgtgtacaagttatctcttttgatgcagactgttttctgtctgattgttaagataatactgatttaaggaagtgatttttttcatgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGATAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - -tgtgtac
- - - - - - - - - - - - - - - tgcagac
- - - - - - - - - - - - - - - - - - - - -ttctgtc