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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgattttccaagtagtgagtttgtcaggtttatgcaaagcatagttgtttcatggcatggtatttgttttgtgaatgctgatgagtttatggttatggttcacactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCAGAAATCATAGAGTATCTAAGAGCAACATACGCTCTTTAGTAAGTGATGC

Basic information

species Glycine max
transcript GLYMA0084S00210.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0084S00210.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 11
gtacgtgattttccaagtagtgagtttgtcaggtttatgcaaagcatagttgtttcatggcatggtatttgttttgtgaatgctgatgagtt--tatggttatggttcacactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCAGAAATCATAGAGTATCTAAGAGCAACATACGCTCTTTAGTAAGTGATGC
     |  |  |    ||  || |    | |   | ||  |  ||||  || |    |    ||  || ||   |  ||||| | |    ||  | |   |     |     | ||||||||||| ||| |||||||||||||||||  |  ||||||||||||||||||||||  | || ||||||| ||||||||| |||||| | ||||  |   
--gtatcctcctttttgttctgtgacaattattctcatctatggcatttttttcatttattgtgtcatatggcata-gaatggtaaaagattgttttaactcctactatggttgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCAGAAATTGTGGAATATCTAAAAGCAACATATGCTCTTCAATAAGCAAAAA
















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|31466779|gb|CD408807.1|CD408807
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCNAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|120495393|gb|EH223560.1|EH223560
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|213615448|gb|DB965520.1|DB965520
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGAT
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGAT
EST: gi|19348874|gb|BM893406.1|BM893406
EST:     AGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|209724770|gb|BW672552.1|BW672552
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|209707531|gb|BW664990.1|BW664990
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|214006768|gb|DB987650.1|DB987650
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|209727805|gb|BW658729.1|BW658729
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|192314929|gb|FK010747.1|FK010747
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|15662186|gb|BI699557.1|BI699557
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|214009602|gb|DB988311.1|DB988311
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|51343312|gb|CO984045.1|CO984045
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|31465032|gb|CD407060.1|CD407060
EST:     GGGGTAGCCCNAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|120529184|gb|EH257318.1|EH257318
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|5752808|gb|AI960095.1|AI960095
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGNAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
EST: gi|5761024|gb|AI966387.1|AI966387
EST:     GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAG                         GCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA
genomic: GGGGTAGCCCAAAGAGACATATACTTTATCAGAAAACTGGAACTTTCCAGgtacgtgatt ... acactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtatttgttttgtgaatgctgatgagtttatggttatggttcacactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCAGAAATCATAGAGTATCTAAGAGCAACATACGCTCTTTAGTAAGTGATGC
                   tgctgat  putative branch site (score: 3)
     atttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgattttccaagtagtgagtttgtcaggtttatgcaaagcatagttgtttcatggcatggtatttgttttgtgaatgctgatgagtttatggttatggttcacactcacagGCACCTTTTTTGGAAGATCCAAACACTGGGATAGAAATGTTTGAAAGTGCAGAAATCATAGAGTATCTAAGAGCAACATACGCTCTTTAGTAAGTGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA