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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatgcttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG

Basic information

species Glycine max
transcript GLYMA18G04170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 3
tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatgcttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG
      || | |   |||      ||   |      | |  ||   | |  | ||||  |  |||    ||      ||   | | |   ||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||| ||  | 
--gtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgctgatatggagtgacatattg--gaatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA-

upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g38370.3 (Oryza sativa), 3'ss of exon 3
tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatgcttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG-------------------
      || | |   |||      ||   |      | |  ||   | |  | ||||  |  |||    ||      ||   | | |   ||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||| ||  ||                   
--gtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgctgatatggagtgacatattg--gaatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAGTCTGTTGCTATTTCTCCTA

upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g62610.1 (Oryza sativa), 3'ss of exon 5
-tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatgcttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG
 |  |   ||         || |  |  | ||||  | |||    ||  ||   ||||  |  ||   | || |  |    |      |  |||||||||| |||||||| || || ||||||||||||||||| |||||   |||||| || |||||||| || || ||||| 
gtaaatggatgaactgttcgctagttcattatgat-caatagcccaaacagttcttttgctgataatac-tgttgttaaattggacacctgagGTTGGAGAGGTTGCAAAGATCACATGCAAGCCAGAATATGCTTATGGAGCTGCAGGTTCACCTCCAGAGATACCGCCAGA-

upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 2
tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatgcttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG
        || |  ||| |    | | |   |        ||| |  |    | | | |  |  |||   || ||||    ||  ||   ||||||| || ||||||||||| || |||||  ||||||||||||||||   |||||| || || ||||| || |||||  | 
-------gta-tgtcaacgtttgcgtctctcgctttggcctttcaccatctctgtgtgacatggtctg--gcatatccaaaaaaatta--agGTTGGCGAGGTTGCAAAAATTACATGCAAATCAGAATATGCATATGGAGCTGCAGGCTCACCACCAGAGATACCTCCTAA-

upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G55520.1 (Arabidopsis thaliana), 3'ss of exon 3
tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatgcttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG
        |    ||||     | | ||  |   |   |  |    | |  | ||    | |||| |    || || || |  ||||  ||||||||||||||||||||||| || || |||||||||||||| || || || || || |||||||| || || || || || 
-------gtttctacaattttgagtctttcttctatccttataatctgaacgcttcagttattatatacaactgatttgattttttttacagGTTGGAGAAGTTGCAAAAATTACATGTAAGCCAGAATATGCTTACGGAAGAGCCGGGTCTCCTCCCGACATCCCACCTGA-

upper sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 3
-tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatg--cttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG
 |  | | ||  | |||     | |||   ||   |   | | ||  ||| | |      |  | |  ||||  ||| | || |  || | ||||||||| || ||||||||||| |||||||||||||| || ||||| ||   ||| || ||||| |||||||| ||| |||| 
gttaatctattcttacagctttatcttgccat---atcttttctggttaaagttgaaagttcctgttacatgttcttttatgttgtttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA-

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|298193802|gb|HO040450.1|HO040450
EST:     AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
EST: gi|298188914|gb|HO035607.1|HO035607
EST:     AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
EST: gi|5676869|gb|AI937999.1|AI937999
EST:     GGCTTGGGAAATTGCAGTGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: GGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
EST: gi|298175755|gb|HO018352.1|HO018352
EST:     AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
EST: gi|21887331|gb|BQ740544.1|BQ740544
EST:     AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
EST: gi|298169599|gb|HO020959.1|HO020959
EST:     AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
EST: gi|298171704|gb|HO021296.1|HO021296
EST:     AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGGGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAATTAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
EST: gi|298185077|gb|HO030290.1|HO030290
EST:     AAAGGGCAGTGTTATCAATGCTTGGGAAATTGCAGTGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
EST: gi|298169647|gb|HO021007.1|HO021007
EST:     AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
EST: gi|18726884|gb|BM523811.1|BM523811
EST:     AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGG                         TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG
genomic: AAAGGGCAGTGTTATCAAGGCTTGGGAAATTGCAGTGAAAACCATGAAGGtctagcaata ... ttttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgaataagggtttttaattttatctcatgcttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG
                                       tgctaat  putative branch site (score: 2)
                                             ttttccc  CT-rich tract
      aataagggtttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatgcttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG

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