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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacattagtgctcagatggcttctgctttggcttgtgccttttctaatgattggtttttagttttaaacagttttgagattttggacttttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTGGGAAAGTTTCTAGAGCATGCTGTTGACTCAGGGATGCTTGTCCTTCAGG

Basic information

species Glycine max
transcript GLYMA16G23830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23830.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0039g00310.t01 (Vitis vinifera), 3'ss of exon 1
tcacattagtgctcagatggcttctgctttggcttgtgccttttctaatgattggtttttagttttaaacagttttgagattttggacttttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTGGGAAAGTTTCTAGAGCATGCTGTTGACTCAGGGATGCTTGTCCTTCAGG
                        | || |    | | |  | |||  || ||| |  |  |  ||   ||||| |   | ||   |    |   || |||| |  |||||||| |||||| | ||||||||||| |||||||||||| |||| ||||| ||||| |||||||| ||||||||| ||||  | ||||| |
-----------------------gtactcttctctctcctctctcttttg-ttgctgctatgcatt---cagttctctaaattaaaa----taactccagGGCAAACCTGGAGTGACTGGATCTGTGATGTGGGATAGTGGAGTTGTATTGGGGAAGTTCCTAGAACATGCTGTGGACTCAGGGCTGCTGCTTCTTCAAG
















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|192316526|gb|FK006789.1|FK006789
EST:     TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTG                         GGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
genomic: TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTGgtatctctct ... ttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
EST: gi|192323275|gb|FK015281.1|FK015281
EST:     TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTG                         GGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
genomic: TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTGgtatctctct ... ttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
EST: gi|192325558|gb|FK019414.1|FK019414
EST:     TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTG                         GGAACGCCTGGAGTAACTGGAGCGGTGATGTGGGACAGTGGAGTTGTACTG
genomic: TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTGgtatctctct ... ttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
EST: gi|151398193|gb|EV268071.1|EV268071
EST:     TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCTTTG                         GGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
genomic: TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTGgtatctctct ... ttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
EST: gi|192299385|gb|FG988727.1|FG988727
EST:     TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTG                         GGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
genomic: TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTGgtatctctct ... ttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
EST: gi|298184617|gb|HO029830.1|HO029830
EST:     TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTG                         GGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
genomic: TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTGgtatctctct ... ttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
EST: gi|192316527|gb|FK006790.1|FK006790
EST:     TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTG                         GGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
genomic: TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTGgtatctctct ... ttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
EST: gi|192326302|gb|FK015864.1|FK015864
EST:     TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTG                         GGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG
genomic: TCGACTCTTGTGGCCACTCTCTCTCCATTCTTCAATCCCCTTCCTCATTGgtatctctct ... ttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgattggtttttagttttaaacagttttgagattttggacttttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTGGGAAAGTTTCTAGAGCATGCTGTTGACTCAGGGATGCTTGTCCTTCAGG
 ttctaat  putative branch site (score: 2)
                                          cttttgtttc  putative PPT
          tttttagttttaaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacattagtgctcagatggcttctgctttggcttgtgccttttctaatgattggtttttagttttaaacagttttgagattttggacttttgtttcaagGGAACGCCTGGAGTAACTGGAGCAGTGATGTGGGACAGTGGAGTTGTACTGGGAAAGTTTCTAGAGCATGCTGTTGACTCAGGGATGCTTGTCCTTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - -ttagtgc
- - - - - - - - - - cttctgc
- - - - - - - - - - - - - - - - cttgtgc