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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaataattacactcattcctttccaaccatcatttacgtcaataaactttcacattttgaaattctccaatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG

Basic information

species Glycine max
transcript GLYMA20G37330.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G175563_T01 (Zea mays), 3'ss of exon 8
gtatgaaataattacactcattcctttccaaccatcatttacgtcaataaactttcacattttgaa--attctccaatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG
||| | |  |||   |   ||| | ||   |      |||   |   |   | | | |||    ||  | | |    | |  |||| |  || ||||||||| | ||||| ||||  ||||||||||||||||||||||| || ||||||||  |  ||||||| || || ||||||||||||
gtaaggatgaatattatatatttcattgatat----gtttgttttgttgttcctgctcataaaaaaccacttttttctcttaagGCCAAAGGTATGAATTGCCTGCACACTAGCATGCCTACAATTGTTCATCGAGATCTGAAATCTCCAAACTTGCTGGTTGACAATAATTGGAATGTTAAG

upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------gtatgaaataattacactcattcctttccaaccatcatttacgtcaataaactttcacattttgaaattctccaatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG
           |  | | |||   ||   |||  |   |   |  | ||||      |  |      | |||    | |  |   | || ||||| | ||| ||||| |||||||||||||| ||||| |||||||||||||| ||||| ||  | ||||| |||||||||||||| |||||||||||||||
gtagaaaaatagattcatatatcaacttccatgtcccccaggc--ttatttcttcagaatagtcactaaattccagactattgttactttcagGCAATGGGGATGAACTGCTTACACACCAGTACACCGACAATTGTTCATCGTGATCTCAAAACACCAAACCTTTTGGTTGATAACAACTGGAATGTTAAG

upper sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 8
gtatgaaataattacactcattcctt--tccaaccatcattt-acgtcaataaactttcacattttgaaattctccaatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG
|||  ||| ||| |  ||  ||| ||  || ||  | ||||| |  ||  ||     ||  |||    ||  || |  | | ||||| | ||| |||||||| || ||||||||   ||| ||||||||||| || ||| | ||||| ||||||||  |||||||||||||||||||||| |||
gtacaaaacaatcaacctacttcattcttctaatgagcattttatatcttta-----tctaattccagaa--ctgctgtgtgcagGCAAAGGGTATGAATTGTTTGCACACCAGTTTACCAACAATTGTTCACCGGGATTTGAAGTCACCAAATCTGCTGGTTGATAAGAACTGGAATGTCAAG

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|6566093|gb|AW233853.1|AW233853
EST:     CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTG                         GCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
genomic: CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTGgtatgaaata ... caatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
EST: gi|9564976|gb|BE474476.1|BE474476
EST:     CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTG                         GCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
genomic: CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTGgtatgaaata ... caatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
EST: gi|51338473|gb|CO982339.1|CO982339
EST:     ATCAGATTGATGAGAAACGAAGAATAAAAATGNNNCTGGATGTG                         GCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
genomic: ATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTGgtatgaaata ... caatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
EST: gi|298181852|gb|HO026027.1|HO026027
EST:     CTAATTGTCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTG                         GCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
genomic: CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTGgtatgaaata ... caatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
EST: gi|19054297|gb|BM732964.1|BM732964
EST:     CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTG                         GCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
genomic: CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTGgtatgaaata ... caatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
EST: gi|33389731|gb|CA852938.1|CA852938
EST:     CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTG                         GCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
genomic: CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTGgtatgaaata ... caatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
EST: gi|151393400|gb|EV263275.1|EV263275
EST:     CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTG                         GCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA
genomic: CTAATTATCAGATTGATGAGAAACGAAGAATAAAAATGGCTCTGGATGTGgtatgaaata ... caatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaccatcatttacgtcaataaactttcacattttgaaattctccaatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG
                                        ttctcc  CT-rich tract
                               attttgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaataattacactcattcctttccaaccatcatttacgtcaataaactttcacattttgaaattctccaatttacagGCTAGGGGCATGAATTGCTTACACACCAGCACACCTACAATTGTTCATCGAGATCTAAAGTCTCCAAATCTTTTGGTTGATAAGAACTGGAATGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC