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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggttagtgggattcagagattaatatatatatatttttagatttgttataatgttatatgaaactgttggttactaattgatataaaatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA

Basic information

species Glycine max
transcript GLYMA18G46390.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g58580.2 (Oryza sativa), 3'ss of exon 6
ggttagtgggattcagagattaatatatatatatttttagatttgttataatgttatatgaaactgttggttactaattgatataaaatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA-
                   | | |  | | |  | | ||   |  ||   ||    |  | ||| | |  |||   |   |   |   | |  | ||||| ||||| ||||||||||| ||||| |||||||||||||| || || ||  |||||||||| ||||||||| | ||||||||||| || ||||| || 
------------------gtcagtgaacaaacctatcta--ctaattcccat----tgggcaacagctccttatggaccaaataactgtttcatcagGGGTACATTCATAGAGTTCCGAAGTGGAATGCTGAATGTGTCGCCCATAGGGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAG

upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 7
ggttagtgggattcagagattaatatatatatatttttagatttgttataatgttatatgaaactgttggttactaattgatataaaatattt--ttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA-
           |      ||||   | |  |    ||  ||||||   ||   || |  |  ||| |||      |  | ||||    |  ||  | ||||| ||||| ||||||||||| ||||| ||| | ||||| || ||||| ||  |||| ||||||||||||||| | ||||| |||||||| || || || 
----------gtcagtcaattatcctgtccaacagttatgatttgcattagc-ttgttagttactattgaccttca--taatattggctgattgctcagGGGTACATTCATAGAGTTCCGAAGTGGAATGATTAATGTATCTCCTATAGGAAGAAACTGTAGCCAAGAAGAACGGGATGAATTTGAGAAGTACGATAAG

upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G45790.1 (Arabidopsis thaliana), 3'ss of exon 5
ggttagtgggattcagagattaatatatatatatttttagatttgttataatgttatatgaaactgttggtt-actaattgatataaaat----atttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA-
                 |  |||  |  ||  |  |     | | | || ||||| |   ||    |  | | | | |||    | ||||    ||   ||||||||||||||| || ||||| | ||| ||||| ||||| ||||| ||||| || || || |||||||||||||||||||| ||||||| |||||| || 
-----------------gtataacgtggatccaactgctagtctctaatcatgtt-tgcaaagtgataagatgatttattttcttgaaatttgtatacatagGGGAACATTTATTGAATTCCGAAATGGAATGCTCAATGTATCACCCATTGGTCGCAACTGCAGCCAAGAAGAAAGAGATGAATTTGAGAGATATGATAAG

upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 6
ggttagtgggattcagagattaatata-tatatatttttagatttgttataatgttatatgaaactgttggttactaattgatataaaatattttt-aGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA-
                   |||  | |  | | |  |  | |   ||||| |  ||| ||  |    ||| |   |   |    |||  | || || |||||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| ||||| || ||||| |||||  | ||||||||||| || |||||||| 
------------------gttagcaaagcagaaacctgaatagcagttattaatttacatttag--attgatacgttcctctcttaatttcttcttcagGGGAACCTTTATAGAGTTCCGAAGTGGGATGCTCAATGTATCACCAATTGGGCGAAACTGCAGCCAGGAAGAGCGTGATGAGTTTGAAAAGTATGACAAG

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|7284889|gb|AW597376.1|AW597376
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|213618074|gb|DB963707.1|DB963707
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|151402864|gb|EV272677.1|EV272677
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|192303883|gb|FG998235.1|FG998235
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|213617059|gb|DB961539.1|DB961539
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|16348803|gb|BI974398.1|BI974398
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|192298879|gb|FG987624.1|FG987624
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATACTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|213592632|gb|DB979423.1|DB979423
EST:     TTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|298189249|gb|HO037652.1|HO037652
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|192306997|gb|FG999988.1|FG999988
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|197664690|gb|FD480363.1|FD480363
EST:     TATTAACTTTACACTTCATTATATTGCTGATCTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|31469416|gb|CD411444.1|CD411444
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|192306982|gb|FG999987.1|FG999987
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|6727118|gb|AW311472.1|AW311472
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|151394726|gb|EV264597.1|EV264597
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|192299912|gb|FG991786.1|FG991786
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|151402943|gb|EV272756.1|EV272756
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|31467953|gb|CD409981.1|CD409981
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
EST: gi|192303884|gb|FG998236.1|FG998236
EST:     TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA                         GGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG
genomic: TATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAggttagtggg ... aatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttataatgttatatgaaactgttggttactaattgatataaaatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA
                                               tattttt  CT-rich tract
                         ttggttactaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttagtgggattcagagattaatatatatatatttttagatttgttataatgttatatgaaactgttggttactaattgatataaaatatttttaGGGGAACATTTATAGAGTTCCGTAGTGGGATGCTGAATGTGTCACCTATTGGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG