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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtacataaaaatttagggggaccgtacagtcatatgttccaatatactgttattagattttaatcttaattacgtatgttgtctttcccccttttccagTTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATG

Basic information

species Glycine max
transcript GLYMA08G21360.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21360.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G062638_T03 (Zea mays), 3'ss of exon 13
-----ggtacataaaaatttagggggaccgtacagtcatatgttccaatatactgttattagattttaatcttaattacgtatgttgtctttcccccttttccagTTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATG
     | | | |   | | |     |    || |  ||  |         |  | |||||   ||  | | ||    | | |   |   ||||  | | || ||||| ||||||| | ||||| ||||||||| ||||||| ||||| ||  | |||||||||||||| ||| | |  
ctatggtttcttgtcattcttttctgtatataaaagcaggtaggtaggcctgtttttatt---ttccactatt--ccaagaaatcttcttttcttcttatttcagTTTCTTGGAATTTCCTATCCCAAATGACGTTGCATTTATTGGAGAGGTCGGCCTTGGTGGTGAACTTAGAACT

upper sequence: GLYMA08G21360.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0002g03180.t01 (Vitis vinifera), 3'ss of exon 16
ggtacataaaaatttagggggaccgtacagtcatatgttccaat-atactgttattagattttaatcttaattacgtatgttgtctttcccccttttc--cagTTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATG
  |   |     || |      || | |  | ||    |||||| ||    | | ||  |||   | ||   ||  |   |   |   |    |||||  ||| | ||||||  | |||||||| |||| ||||||||||||||| || || |||||||||||||||||||||| |
--tttcttttctttcatctcttcctt-ctttaatcccctccaatgatgaattcactacttttctttgttgtataaatcaatgaacaaactttgttttcttcagCTTCTTGGAGTTTCCTATTCCCAATGGCATTGCATTCATTGGAGAGATCGGCCTTGGTGGTGAGCTTCGCACG

upper sequence: GLYMA08G21360.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0002g03190.t01 (Vitis vinifera), 3'ss of exon 13
ggtacataaaaatttagggggaccgtacagtcatatgttccaatatactgtt-attagatttta--atcttaattacgtatgttgtctttcccccttttccagTTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATG
 ||   |     || |      || | |  | ||    |||||| |    || | ||   |||    |  ||| |   |    ||   ||     | ||| || | ||||||  | |||||||| |||| ||||||||||||||| ||||| |||||||||||||||||||||| |
-gtttcttttctttcatctcttcctt-cttttatcccctccaatgtcaaattcactattctttgtcgttataaatcaatgaactgaactttgttttcttc-agCTTCTTGGAGTTTCCTATTCCCAATGGCATTGCATTCATTGGAGAAATCGGCCTTGGTGGTGAGCTTCGCACG

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|51336133|gb|CO979999.1|CO979999
EST:     CTGACTGAGACTGCAGGAGATCTAGCTATAGCAGCAGCAATTTGCAGCAG                         TTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGG
genomic: CTGACTGAGACTGCAGGAGATCTAGCTATAGCAGCAGCAATTTGCAGCAGgtttttgttt ... ccttttccagTTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgttattagattttaatcttaattacgtatgttgtctttcccccttttccagTTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATG
                   tcttaat  putative branch site (score: 3)
                              tatgttgtctttcccc  putative PPT
     ttattagattttaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtacataaaaatttagggggaccgtacagtcatatgttccaatatactgttattagattttaatcttaattacgtatgttgtctttcccccttttccagTTGCTTGGAAATCCCTATTCCAAATGACATTGCATTCATTGGTGAAATTGGCCTTGGTGGTGAGCTTCGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - -ataaaaa
- - - - - - - taggggg
- - - - - - - - - - - - - - - -catatgt