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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtaagtcgagatgttcttttgttgagatatttgtggaccaatttttttgtttacttggttagtctctaattgatttttgtgatgttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTCATGGAAGCCTTGGCTGCTGGTGCTGATGTTAGTATGATTGGACAGTTTG

Basic information

species Glycine max
transcript GLYMA18G08220.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0194g00030.t01 (Vitis vinifera), 3'ss of exon 2
------ggtaagtcgagatgttcttttgttgagatatttgtggaccaatttttttgtttacttggttagtctctaattgatttttgtgatgttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTCATGGAAGCCTTGGCTGCTGGTGCTGATGTTAGTATGATTGGACAGTTTG-
       || | | ||  |  | |||  ||  |  || ||  |      |||         || ||| ||    ||    | ||| |||||| || |  ||||  |||| |||||| | || || ||||| |||||||| |||||||| ||||||||||| || ||||||||||||||||| || |||||||||||||||| 
gtgagtagtgatttgaagtaat-tttcattttgtaatgtgatgcttgcctttgaatggccttttgtttgttgacaaaatctatttctgatgtgttctg-cagACCTGGTGAACAACCTTGGGACCATTGCAAGGTCTGGAACCAAGGAGTTCATGGAAGCTTTAGCTGCTGGTGCTGATGTGAGCATGATTGGACAGTTTGG

upper sequence: GLYMA18G08220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0015g01090.t01 (Vitis vinifera), 3'ss of exon 2
--------ggtaagtcgagatgttcttttgttgagatatttgtggaccaatttttttgtttacttggttagtctctaattgatttttgtgatgttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTCATGGAAGCCTTGGCTGCTGGTGCTGATGTTAGTATGATTGGACAGTTTG-
            ||| |     | | | || |     |||  |  |  ||  |||     |  |   |  ||| ||||||  | | ||   |   |  ||||||||||||| |||||| | ||||| |||||| | || || ||||| ||||||||||||||| |||||||||||||||||||||| |||||||| ||||||| 
gtaagcagaaatagtagtagcatgcatatggtttatcattattttataaacatttgaaactgatgtttatgtccctaattattatctgctgttaatgctttcagATTTGGTGAACAACCTTGGTACCATTGCTCGATCAGGAACCAAAGAATTCATGGAAGCCCTGGCTGCTGGTGCTGATGTTAGCATGATTGGGCAGTTTGG

upper sequence: GLYMA18G08220.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29061 (Selaginella moellendorffii), 3'ss of exon 2
ggtaagtcgagatgttcttttgttgagatatttgtggaccaatttttttgtttacttggttagtctctaattgatttttgtgatgttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTCATGGAAGCCTTGGCTGCTGGTGCTGATGTTAGTATGATTGGACAGTTTG-
                         |  | | |     ||| || ||     ||   ||  |||   || |||     | || |  || |||  |||| | || |||||| | || |||||||| |||||||| |||||||| ||||||||||||||||| ||||| || |||||    ||||| || ||||||| 
-----------------------gtaagtttctagcttccagttcttcc---tagccgg--agttcttacttg-----tatgctcattctttctagATCTCGTGAACAACCTCGGCACAATTGCCAGGTCTGGCACCAAGGAGTTCATGGAAGCCTTGGCCGCTGGCGCCGATGTGTCCATGATCGGTCAGTTTGG

upper sequence: GLYMA18G08220.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17594 (Selaginella moellendorffii), 3'ss of exon 2
ggtaagtcgagatgttcttttgttgagatatttgtggaccaatttttttgtttacttggttagtctctaattgatttttgtgatgttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTCATGGAAGCCTTGGCTGCTGGTGCTGATGTTAGTATGATTGGACAGTTTG-
                         |  | | |     ||| || ||     ||   ||  |||   || |||     | || |  || | |  |||| | || |||||| | || |||||||| |||||||| |||||||| ||||||||||||||||| ||||| || |||||    ||||| || ||||||| 
-----------------------gtaagtttctagcttccagttcttcc---tagccgg--agttcttacttg-----tatgctcattctctctagATCTCGTGAACAACCTCGGCACAATTGCCAGGTCTGGCACCAAGGAGTTCATGGAAGCCTTGGCCGCTGGCGCCGATGTGTCCATGATCGGTCAGTTTGG

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|193473569|gb|FK437186.1|FK437186
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|151402250|gb|EV272063.1|EV272063
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|193531217|gb|FK487948.1|FK487948
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|13125720|gb|BG316290.1|BG316290
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|298180770|gb|HO022209.1|HO022209
EST:     CTAACAATTCGCTGACCATTGTTGCCAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|10846004|gb|BF068997.1|BF068997
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAAACAACTTGGG
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAA-CAACTTGGG
EST: gi|10845994|gb|BF068991.1|BF068991
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         TATTTGGGTAAACAACT
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGG-TAAACAACT
EST: gi|193309837|gb|FK274545.1|FK274545
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGG
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGG
EST: gi|57574579|gb|CX547554.1|CX547554
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|7685027|gb|AW755675.1|AW755675
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|192297125|gb|FG988221.1|FG988221
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|16996959|gb|BM086331.1|BM086331
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|208285234|gb|GE089086.1|GE089086
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
EST: gi|9987183|gb|BE661291.1|BE661291
EST:     CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCT                         GATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC
genomic: CTAACAATTCGCTGACCATTGTTGACAGTGGCATTGGCATGACCAAAGCTggtaagtcga ... ttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttttttgtttacttggttagtctctaattgatttttgtgatgttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTCATGGAAGCCTTGGCTGCTGGTGCTGATGTTAGTATGATTGGACAGTTTG
                                           tgttttttttc  CT-rich tract
                         tctaattgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaagtcgagatgttcttttgttgagatatttgtggaccaatttttttgtttacttggttagtctctaattgatttttgtgatgttttttttcaGATTTGGTAAACAACTTGGGTACAATTGCTAGGTCTGGTACCAAGGAATTCATGGAAGCCTTGGCTGCTGGTGCTGATGTTAGTATGATTGGACAGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT