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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTATGCGCAGCTCAACAAACCCGATCAAGAGAGACCCCCTTTACCCGTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttcttttcttcctcatttttttgtgccctttttgtcaatatatgaaaagtttgtaaatttgattattctataacatggggttgaaaattttggg...

Basic information

species Glycine max
transcript GLYMA10G06240.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G06240.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv08s0007g05070.t01 (Vitis vinifera), 5'ss of exon 2
TGGTTTATGCGCAGCTCAACAAACCCGATCAAGAGAGACCCCCTTTACCCGTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttcttttcttcctcatttttttgtgccctttttgtcaatatatgaaaagtttgtaaatttgattatt-ctataacatggggttgaaaattttggg--
              || ||||| || ||    ||||     || || ||||| ||||||||||| |||||||||||||| ||||| ||| | |||||||||||  |||   || ||| ||    | || |      |||  |  |       |||||||||  ||||    || || |    |  | |  ||  |  | |   
--------------CTTAACAAGCCAGAGGGTGAGAAGAAGCCCTTGCCCGTTGACGAAGATTTACCTGGGATGGGCCAATACTACTGCTTGCACTGCGAgtatgttttcctttttcttctgaatcttctctttcctttacctgtgccc---aagtttgtaggtttggggtttacttttttgtaagatgcaagctaatagaat

upper sequence: GLYMA10G06240.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S37_98V6.1 (Physcomitrella patens), 5'ss of exon 2
---TGGTTTATGCGCAGCTCAACAAACCCGATCAAGAGAGACCCCCTTTACCCGTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttcttttcttcctcatttttttgtgccctttttgtcaatatatgaaaagtttgtaaatttg---attattctat-aacatggggttgaaaattttggg
   || || |  |  | ||   ||||   ||   |  || | |       |   ||||   ||||||||| || |||||||||| |||||||||||||||||||||| |  |  |        |||      ||   | | || ||   | || || ||    || |  |   | |  | ||| || | |  |      | | | | 
ACATGATTCACACAGAACTTCGCAAAGTGGAGACACCGAAATCTAAGGAGC---TCGATCCAGATTTGCCGGGCATGGGCCAGTTCTATTGCCTTCACTGCGAgtaagtcacaatgtacatagattgc---atgtaatatctgacagcctgtgcaatgtac-caactcgggcaactgatgtattaataggtagccagccaatatagc
















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|193428279|gb|FK395369.1|FK395369
EST:     GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGA
genomic: GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGA
EST: gi|193400694|gb|FK368335.1|FK368335
EST:     GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGA
genomic: GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGA
EST: gi|151413206|gb|EV283014.1|EV283014
EST:     GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
genomic: GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
EST: gi|51335550|gb|CO979416.1|CO979416
EST:     GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
genomic: GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
EST: gi|193319111|gb|FK285961.1|FK285961
EST:     GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGA
genomic: GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGA
EST: gi|193401238|gb|FK366821.1|FK366821
EST:     TATTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
genomic: TATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
EST: gi|23727880|gb|BU761975.1|BU761975
EST:     GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
genomic: GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
EST: gi|57574280|gb|CX547255.1|CX547255
EST:     GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
genomic: GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
EST: gi|193339438|gb|FK304785.1|FK304785
EST:     GTACTTTTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
genomic: GTACTATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
EST: gi|58015348|gb|CX702090.1|CX702090
EST:     GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGA                         TCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG
genomic: GTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttct ... atttgtgcagTCGGTACTTTGCCAATATAACTGTGAGGGATGAGCACTTTAAGACCAAACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTATGCGCAGCTCAACAAACCCGATCAAGAGAGACCCCCTTTACCCGTCGACGAAGATTTGCCTGGGATGGGCCAGTACTATTGCCTTCACTGCGAgtaattttcttttcttcctcatttttttgtgccctttttgtcaatatatgaaaagtttgtaaatttgattattctataacatggggttgaaaattttggg

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggttg