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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattttgaacatagaatataggcaatatatgaatgtacatactttagctagcagctgcacagcttcacaatctaattttgacatgcttctttactttttgcccagTGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACTACCTGAAATATGGAGAGAATGACTATTATCCACCTCTTCCAAATGGTCA

Basic information

species Glycine max
transcript GLYMA08G01850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01850.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G009070_T01 (Zea mays), 3'ss of exon 2
gtatgtattttgaacatagaatataggcaatatatgaatgtacatactttagctagcagctgcacagcttcacaatctaattttgacatgcttctttactttttgcccagTGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACTACCTGAAATATGGAGAGAATGACTATTATCCACCTCTTCCAAATGGTCA
               || || | |    ||||| | ||| |  | |    | || | |   |  ||   ||||  |    |||  |||   || ||    | ||   |||| || ||  | ||||||||||| || || ||||| ||||| ||| | || ||| |||||||||| |  ||||| ||||| ||||| ||||||||||| ||
-------------gtat-gattcttaataatatct-aatatgtagaacagatctgg-attagtgcattatcaccctggtttttacacaaatttgttgttctattctgcagTAGATATCCTAGATGATATGTTGGCAGGTGTAGGCTGGACTATGGAAGAATACTTGAAATATGGTGCTAATGATTATTACCCACCCCTTCCAAATGGGCA

upper sequence: GLYMA08G01850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g03410.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtattttgaacatagaatataggcaatatatgaatgtacatacttta-gctagcagctgcacagcttcacaatctaattttgaca--tgcttctttactttttgcccagTGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACTACCTGAAATATGGAGAGAATGACTATTATCCACCTCTTCCAAATGGTCA
           | ||| | | |  | | ||  |   ||  ||  | || || | ||| | |   ||    |   |  |||||||| |||  ||  | ||| | | ||   |||||||||| |||||||||||||| ||||| || |||||||| ||||| || ||| |||||||||| |  ||||| || || || ||||||||||| |||||
----------agtacacacactggaagtaaagtgataagata-gtgctgtatgttagtacca--accatctggaagcctaattttaacacctggatgttttcatcttcttcagTGGACATCTTGGATGATATGTTGGCTGGCGTGGGATGGACAATGCACGATTACTTGAAATATGGGGCAAATGATTACTACCCGCCTCTTCCAAACGGTCA
















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|26268857|gb|CA819920.1|CA819920
EST:     CTGACATCTGACAATCCCAAGAGTGAAGATCCAT                         TGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACT
genomic: CTGACATCTGACAATCCCAAGAGTGAAGATCCATgtatgtattt ... ttttgcccagTGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACT
EST: gi|193403350|gb|FK367700.1|FK367700
EST:     AAGTGAAGTGACCATGCTGACATCTGACAATCCCAAGAGTGAAGATCCAT                         TGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACT
genomic: AAGTGAAGTGACCATGCTGACATCTGACAATCCCAAGAGTGAAGATCCATgtatgtattt ... ttttgcccagTGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACT
EST: gi|57575436|gb|CX548411.1|CX548411
EST:     AAGTGAAGTGACCATGCTGACATCTGACAATCCCAAGAGTGAAGATCCAT                         TGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACT
genomic: AAGTGAAGTGACCATGCTGACATCTGACAATCCCAAGAGTGAAGATCCATgtatgtattt ... ttttgcccagTGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACT
EST: gi|10233051|gb|BE801939.1|BE801939
EST:     ATCTGACAATCCCAAGAGTGAAGATCCAT                         TGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACT
genomic: ATCTGACAATCCCAAGAGTGAAGATCCATgtatgtattt ... ttttgcccagTGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagctgcacagcttcacaatctaattttgacatgcttctttactttttgcccagTGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACTACCTGAAATATGGAGAGAATGACTATTATCCACCTCTTCCAAATGGTCA
                         ttttgac  putative branch site (score: 3)
                                   cttctttactttttgc  putative PPT
                  aatctaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtattttgaacatagaatataggcaatatatgaatgtacatactttagctagcagctgcacagcttcacaatctaattttgacatgcttctttactttttgcccagTGGACATATTGGATGATATGTTAGCTGGGGTAGGATGGACGATGCAGGACTACCTGAAATATGGAGAGAATGACTATTATCCACCTCTTCCAAATGGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA