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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgatcttaattaagtttcaaattagccaaaaaaatatcttatcttaattaattaatgcgaattgaccgtgaggttgttatttttttatttacagCACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTAAGTTCCAGTTTCGACCACAATCTCCTCGATCTGTTGCTCTTGGGCGTCC

Basic information

species Glycine max
transcript GLYMA19G43450.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G43450.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0081g00010.t01 (Vitis vinifera), 3'ss of exon 4
gttagtgatcttaattaagt----ttcaaattagccaaaaaaatatctta--tcttaattaattaatgcgaattgaccg--tgaggttg-----ttatttttttatttacagCACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAA--ATTTGTAAGTTCCAGTTTCGACCACAATCTCCTCGATCTGTTGCTCTTGGGCGTCC
|||||| || |  | |   |     |||   |    |     || |   |  | || |  | ||     || || | |   ||   |||     ||| |   |    | |||| |||||||||||| | ||||||||||||||||||||||||||   ||    |   | |   |   |  | |  |      | |||  | || |||  |   
gttagtcatatatacttgctgcaactcatgatcattatggttatgttcaaaattttcaccacttttgctgacttaatctcttgtatttgcttgattaatcaatggcatgcagCCCCAAGAGCAGTGGAGAAGTGCAAGAACAGAAGCTAGAGGCACCCATCCACAGTCTGCCCATCAAAGGAAAGCCAGAAGCAGCTGAGGATCATGGATGG--
















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|254334950|gb|GR844735.1|GR844735
EST:     ATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGCGGCAATCGGGCTAG                         CACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTA
genomic: ATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGCGGCAATCGGGCTAGgttagtgatc ... ttatttacagCACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTA
EST: gi|192306533|gb|FG997217.1|FG997217
EST:     ATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGCGGCAATCGGGCTAG                         CACCAAGAGCAGTGCAAA-GTGCA-GA-CAGA-GCTAGAG-CAAATTTGTA
genomic: ATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGCGGCAATCGGGCTAGgttagtgatc ... ttatttacagCACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTA
EST: gi|254318334|gb|GR832502.1|GR832502
EST:     ATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGCGGCAATCGGGCTAG                         CACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTA
genomic: ATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGCGGCAATCGGGCTAGgttagtgatc ... ttatttacagCACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTA
EST: gi|192306534|gb|FG997218.1|FG997218
EST:     ATCATGCAAGCGCCTGCGTATAATGAAAGGATTTGCGGCAATCGGGCTAG                         CACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTA
genomic: ATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGCGGCAATCGGGCTAGgttagtgatc ... ttatttacagCACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTA
EST: gi|57575143|gb|CX548118.1|CX548118
EST:     ATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGCGGCAATCGGGCTAG                         CACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTA
genomic: ATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGCGGCAATCGGGCTAGgttagtgatc ... ttatttacagCACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttaattaattaatgcgaattgaccgtgaggttgttatttttttatttacagCACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTAAGTTCCAGTTTCGACCACAATCTCCTCGATCTGTTGCTCTTGGGCGTCC
                    aattgac  putative branch site (score: 3)
                                     ttatttttttattt  putative PPT
                                  ttgttatttttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgatcttaattaagtttcaaattagccaaaaaaatatcttatcttaattaattaatgcgaattgaccgtgaggttgttatttttttatttacagCACCAAGAGCAGTGCAAAAGTGCAAGAACAGAAGCTAGAGGCAAATTTGTAAGTTCCAGTTTCGACCACAATCTCCTCGATCTGTTGCTCTTGGGCGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC