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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaggggactgttcaatatatagatatagatacctttcccaccccatttctcatatatctattttgggtatacttgtttatttacttgttgttttaacagGGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTTGCAGTGAAGCGTAGACTTGCATGTGAGATGGTGAAATATTGGCAACAG

Basic information

species Glycine max
transcript GLYMA20G35900.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G73390.2 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------------------------------caaggg-gactgttcaatatatagatatagata----cctttcccaccccatttctcatatatctattttgggtatacttgtttatttacttgttgttttaac-agGGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTTGCAGTGAAGCGTAGACTTGCATGTGAGATGGTGAAATATTGGCAACAG
                                                                                     || |    |||  | |  |  |     ||| ||       |         | |  |   |||   ||||   || | ||  || | |||    || | | |   ||||||| ||||| |||||||| ||||| ||||||||| | |||||||||||||| |||||||| |||||| ||||||| ||||||||||| ||||| |||
gtagaatcactttcaatgtttgggatatattaactaattatgatttgctacatgtgttgcctagtttatttgtgaatatcgtcatcatgttcaactacttagaaactcagcctagttagaagtagtgatggttagagtattttaatagacatttatagtcttctatttaagttataaattttctaatttagGGTGTTGATATCCAACTTGGGATGGCGATTGATAGTGCAAAAGCCACTCTTGCCGTGAAGCGAAGACTTTCATGTGAAATGGTGAAATACTGGCAGCAG

upper sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 8
caaggggactgttcaatatatagatatagatac-ctttcccaccccattt--------ctcatata---tctattttgggtatacttgtttatttacttgttgtttt----aacagGGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTTGCAGTGAAGCGTAGACTTGCATGTGAGATGGTGAAATATTGGCAACAG
       ||   ||  |  || |||| || ||  || |||||   ||| |        ||||| ||   ||| | |    | ||     | |  |  ||   ||||     || ||||||| ||||| |||||||| ||||| ||||||||  | || |||||||||||||| || || |||||| ||||||| ||||||||||||||||| |||
--gtaatacctctcctttgatggatagagttaagctatcccatggcatctaactgtacctcatgtagtttctttctctcatttagaatctaacatctttcaagtttctgaaaatagGGTGTTGATATCCAACTTGGCATGGCGATTGATAGCTCAAAGGCCACTCTTGCAGTAAAACGAAGACTTTCATGTGAAATGGTGAAATATTGGCAGCAG

upper sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv16s0039g00390.t01 (Vitis vinifera), 3'ss of exon 9
caaggggactgttcaatatatagatatagatacctttcccaccccatttctcatatatctattttgggtat---acttgtttatttacttgttgttttaacagGGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTTGCAGTGAAGCGTAGACTTGCATGTGAGATGGTGAAATATTGGCAACAG
  |        |||   | | ||  | | | |  |     |    ||||   | | |   |||   || |    |||  | |  || |    |  |   | ||||||| ||||| || ||||||||||| |||||||||||||| || || |||||||| || || || |||||||||||||||||||| |||||||| |||
--acaatgtctttcttaaaaaagggaaaaacatttaatttagttaatttgg-aaacagacattacaggcacttcactgatattctttccaacttctgatatagGGTGTTGATATCCAGCTTGGAATGGCTATTGATAGTACCAAGGCTACACTTGCAGTAAAACGGAGGCTTGCATGTGAGATGGTGAAGTATTGGCAGCAG

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|10710494|gb|BF010212.1|BF010212
EST:     ATCTTGCAGAAGGAGTTCTTCGAGCACTCTGTCTACAAGCATTGGGACAG                         GGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTT
genomic: ATCTTGCAGAAGGAGTTCTTCGAGCACTCTGTCTACAAGCATTGGGACAGgtattcatat ... gttttaacagGGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTT
EST: gi|151398827|gb|EV268698.1|EV268698
EST:     ATCTTGCAGAAGGAGTTCTTCGAGCACTCTGTCTACAAGCATTGGGACAG                         GGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTT
genomic: ATCTTGCAGAAGGAGTTCTTCGAGCACTCTGTCTACAAGCATTGGGACAGgtattcatat ... gttttaacagGGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTT
EST: gi|151404759|gb|EV274573.1|EV274573
EST:     ATCTTGCAGAAGGAGTTCTTCGAGCACTCTGTCTACAAGCATTGGGACAG                         GGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTT
genomic: ATCTTGCAGAAGGAGTTCTTCGAGCACTCTGTCTACAAGCATTGGGACAGgtattcatat ... gttttaacagGGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctcatatatctattttgggtatacttgtttatttacttgttgttttaacagGGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTTGCAGTGAAGCGTAGACTTGCATGTGAGATGGTGAAATATTGGCAACAG
                                           ttgtttt  CT-rich tract
                               tttatttacttgttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaggggactgttcaatatatagatatagatacctttcccaccccatttctcatatatctattttgggtatacttgtttatttacttgttgttttaacagGGTGTAGATATTCAACTTGGAATGGCAATTGATAGTACCAAAGCCACTCTTGCAGTGAAGCGTAGACTTGCATGTGAGATGGTGAAATATTGGCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - -ctttccc