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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttggagtgcttcattaatgagtatcacataatatattatattaagcagtatatttctttgttttttattaccaacttggttttttttttttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGTTGTACTCTTGAT

Basic information

species Glycine max
transcript GLYMA18G52310.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G52310.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G39460.1 (Arabidopsis thaliana), 3'ss of exon 2
acttggagtgcttcattaatgagtatcacataatatattatattaagcagtatatttctttgttttttattaccaacttggttttttttttttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGTTGTACTCTTGAT-
       || ||| |   |  | | |   || |    || |  | ||   |  |||   ||   | |  ||  ||   ||||||  |||| ||     ||||||||||||||| ||||| || || || ||| | || |||||||||||||| |||||||| ||||||||||| || |||||||||||    || |   | 
-------gtactttaaagagtatttttctatgaagccttgttgtgag--attgattatgttcaatatatttgacactatggtttggttttgtt----acagGCCTGATGGAACCAAGAAGGCTTACGTGAGGCTTACACCAGACTATGATGCTTTGGATGTTGCTAACAAGATCGGCATCATCTAAGTCTATCTATCTCTG

upper sequence: GLYMA18G52310.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G55280.1 (Arabidopsis thaliana), 3'ss of exon 3
acttggagtgcttcattaatgagtatcacataatatattata--ttaagcagtatatttctttgttttttattaccaacttggttttttttttttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGTTGTACTCTTGAT--
                              ||| | | || |  || |     ||||   ||| | |   |  |   | |      | | | ||| | |||||||| |||||||||||||| || ||||| ||||||||||| || |||||||| |||||||| |||||||| || || |||||||||  || |   |||    
-----------------------------gtaa-acactaaaacttcactgagatatgggtttatgta--aacatggagtgatgagtgtatgtttgtatgcagGCCCGATGGAACAAAGAAGGCGTATGTGAGGTTGACTCCTGATTATGATGCTTTGGATGTGGCTAACAAAATCGGGATCATCTAATCTG-ATCATTGTCGC

upper sequence: GLYMA18G52310.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04090.t01 (Vitis vinifera), 3'ss of exon 3
---acttggagtgcttcattaatgagtatcacataatatattata-ttaagcagtatatttctttgttttttattaccaacttggttttttttttttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGTTGTACTCTTGAT-
     |||||     | | | |||| ||||       | | | |  ||  || |   | |      ||||  |  ||     ||   ||  ||||| |  | |||||||||||| || ||||| || |||||||||||||| ||||||||||||||||||||||| || ||||| ||||| |||||||||| |    |||   | 
ttagattggataaacttaattatgaatatcctgagcaagaatgttcttttgctgggaaat-----attttcgacaactcttctgacattaatttttgtgatccagGCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGCCTTGGATGTGGCCAACAAAATTGGGATCATCTAAGGTAGGATCTGTCTA

upper sequence: GLYMA18G52310.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
-acttggagtgcttcattaatgagtatcacataatatattatattaagcagtatatttctt-tgttttttattaccaacttggttttttttttttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGTT-GTACTCTTGAT
    |    |   |   ||  |||| |       | |  | | |  ||   ||||  | |  |   |||| ||  | |  |    |||| | |||| || |||||||||||| ||||||||||| |||||||||||||| ||||| |||||||| |||||||| || |||||||||||||| || |||  | |||  |     
tttcttatatatatatatatcgagt-tggtggtgttttctttttccagttttatacctttcctaaattttgtt--ctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA----

upper sequence: GLYMA18G52310.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g00250.t01 (Vitis vinifera), 3'ss of exon 3
acttggagtgcttcatta-atgagtatcacataatatattatattaa-gcagtatatttctttgttttttattaccaacttggttttttttttttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGT-TGTACTCTTGAT
     || || |    || ||| | |||| |  |  |    ||   | |  | ||| |  ||      ||  ||  ||||    || | | ||| | |||||||||||||||||| ||||| || |||||||||||||| || |||||||||||||||||||| || |||||||| || ||||||||| | | || |     |
---cagaatggtgtgatatatgggcatcataccaagtggattagcgatgtggcatagtggttgtcaaattgatatgaactaaccttctatctttgtgttgcagGCCTGATGGAACCAAGAAGGCTTATGTTAGGTTGACACCGGACTATGATGCCTTGGATGTGGCAAACAAGATCGGGATCATCTAAATCTATATTGCCTTT

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|10231198|gb|BE800014.1|BE800014
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACANAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|6912851|gb|AW394335.1|AW394335
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|58023430|gb|CX710171.1|CX710171
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|21675568|gb|BQ627919.1|BQ627919
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|298183127|gb|HO028390.1|HO028390
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|58023747|gb|CX710488.1|CX710488
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|6912844|gb|AW394328.1|AW394328
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|58021757|gb|CX708498.1|CX708498
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|9985660|gb|BE659768.1|BE659768
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAA-GTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|15813989|gb|BI786264.1|BI786264
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|58023732|gb|CX710473.1|CX710473
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
EST: gi|7147034|gb|AW508956.1|AW508956
EST:     TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCA                         GGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG
genomic: TGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa ... tttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcagtatatttctttgttttttattaccaacttggttttttttttttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGTTGTACTCTTGAT
                               cttggttttttttttt  CT-rich tract
                 ttttttattaccaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttggagtgcttcattaatgagtatcacataatatattatattaagcagtatatttctttgttttttattaccaacttggttttttttttttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGTTGTACTCTTGAT

- - - - tgcttca
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