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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgtggtagaggaatttccataggatccacttataataccaaataagaaattgcttattttgtctgcacataaatttgttgacaattatcctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACAATCATGGCTTCAAGACAATCAAATCCTTCTCGGAGATCTAAGATCAGTA

Basic information

species Glycine max
transcript GLYMA12G35390.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G574782_T01 (Zea mays), 3'ss of exon 11
---------ggtgtggtagaggaatttccataggatccacttataataccaaataagaaattgcttattttgtctgcacataaatttgttgacaattatcctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACAATCATGGCTTCAAGACAATCAAATCCTTCTCGGAGATCTAAGATCAGTA
            |   | |  |  |||   |  | ||  | |||  | | |  ||  |||||    ||| | |||     |  ||||    | |       | |||||||||| ||||||||||| || ||||| || |||||||  || || |||||||||||||| |||   || |||||||| |||   ||||||| ||     | 
tatttgctcatcgcattggttgtgtttttttttgttct-catatttttctacctagaaaatttggaattat-tctctgtgtctatttaaccata-------tctttcagGTTTTGAGGTGATAATCTCCATTCGCCCGGGAAATGCCCCACTTCCTGACAATCATGGTTTCCGCACTATCAAATCATTCAGCGAGATCTGAGGAATCTG

upper sequence: GLYMA12G35390.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 11
ggtgtggtagaggaatttccataggatccacttataataccaaataagaaattgcttattttg------tctgcacataaatttgttgacaattatcctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACAATCATGGCTTCAAGACAATCAAATCCTTCTCGGAGATCTAAGATCAGTA
      |      |  |||| |  |||  |   |       ||| ||    ||  || || ||        | || |   || | |  | | ||| ||  |  |||| |||||||||||||| ||||||||||| ||||||||||| || || || ||||| || ||||||||||||| ||| || || || || | |||  ||  
-----agcctgttacgttcc-tgagataaagaaaaggagggaaaaaaaccgtttgttgttctgattcgtctttcagactgatatttcaatatttacccattggcagGGTTGGAGGTGATAATCTCTATTCGACCAGGAAATGGACCTCTTCCAGATAATCACGGGTTCAAGACAATCACATCTTTTTCAGACATTTGAGACTAGAT
















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|31462181|gb|CD404209.1|CD404209
EST:     TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAG                         GTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
genomic: TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAGgtatgaacat ... cctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
EST: gi|19269465|gb|BM885721.1|BM885721
EST:     GTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAG                         GTTTGGAGGTGATAATTTCTATTCGACCTGGGAATGGACCCCTCCCTGACA
genomic: TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAGgtatgaacat ... cctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
EST: gi|15199320|gb|BI423772.1|BI423772
EST:     TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAG                         GTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
genomic: TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAGgtatgaacat ... cctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
EST: gi|12689440|gb|BG155837.1|BG155837
EST:     TGTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAG                         GTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
genomic: TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAGgtatgaacat ... cctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
EST: gi|58018251|gb|CX704993.1|CX704993
EST:     TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAG                         GTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
genomic: TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAGgtatgaacat ... cctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
EST: gi|16342399|gb|BI967994.1|BI967994
EST:     TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAG                         GTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
genomic: TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAGgtatgaacat ... cctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
EST: gi|22522469|gb|BU081280.1|BU081280
EST:     TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAG                         GTTTGGAGGTGATAATTTCTATTCGACCTGNAAATGGA
genomic: TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAGgtatgaacat ... cctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGA
EST: gi|11274034|gb|BF324402.1|BF324402
EST:     TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAG                         GTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA
genomic: TTTATTTGTCACTGATGTATATCAAGAAGCCACAGCTGCAAAGGCAGCAGgtatgaacat ... cctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaattgcttattttgtctgcacataaatttgttgacaattatcctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACAATCATGGCTTCAAGACAATCAAATCCTTCTCGGAGATCTAAGATCAGTA
                                tgttgac  putative branch site (score: 3)
                                            tcctgtttc  putative PPT
                         ataaatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgtggtagaggaatttccataggatccacttataataccaaataagaaattgcttattttgtctgcacataaatttgttgacaattatcctgtttcagGTTTGGAGGTGATAATTTCTATTCGACCTGGAAATGGACCCCTCCCTGACAATCATGGCTTCAAGACAATCAAATCCTTCTCGGAGATCTAAGATCAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
ggtgtgg
- - - - - - - - - - - - - -ccactta
- - - - - - - - - - - - - - - - - - - -ccaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgac