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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcaggtagttgaaacatttttacagtttcattgcaacatgtgtgagtttcttttgcatttctaggaattgatctgtccttgatgaattatttgcctcagGGGTATTGGCTGAAGAGGCATCAAAGATTGCTTCAACATATAATGATGTTTTTACTGCCAAAATATTAGATGCTGAGCAGTGTAAAGAATTGAAAATGGG

Basic information

species Glycine max
transcript GLYMA19G22730.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 3
ggcaggtagttgaaacatttttacagtttcattgcaacatgtgtgagtttcttttg-----catttctaggaattgatctgtccttgatgaattatttgcct----cagGGGTATTGGCTGAAGAGGCATCAAAGATTGCTTCAACATATAATGATGTTTTTACTGCCAAAATATTAGATGCTGAGCAGTGTAAAGAATTGAAAATGGG
              | |||| |   |||  |   |||   |||    |      |      ||||   | |  ||  | | ||  |  | | | || | | |    |||  ||  | || || ||||||||||| |||||||| ||||| | |||||| || ||||| | |||||||||||  ||| | |||||||| || || |||||
------------gtatatttcttttgttaaacgccaaacagtggatctcctccatagatgccattctgatgttttcttatttcactactcactcatctcctttatccagCTGTGCTTGCCGAGGAGGCATCAAACATTGCTTCTACATACAGTGATGTATTCACTGCGACAATATTAGATGTGGAGAAATGTAAAGAGTTAAAGATGGG

upper sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 3
ggcaggtagttgaaacatttttacagtttcattgcaacatgtgtgagtttcttttgcatttctaggaattgatctgtccttgatgaattattt---gcctcagGGGTATTGGCTGAAGAGGCATCAAAGATTGCTTCAACATATAATGATGTTTTTACTGCCAAAATATTAGATGCTGAGCAGTGTAAAGAATTGAAAATGGG
    |    ||| || | | | |   |||  |  |    ||| ||    | | |  || |||||| | |  | ||||   |  | | |||| |    ||||||||||||| || |||||||| ||||| ||||||||  |||| | ||||||  || | || ||||| || ||||| ||||| || || ||| ||||||||||
--ttgtctattgcaataatatgatc-ttttttgcctttttgtctgttcctgtctgtcaattctagaattctaactgttaattgtcatttatgttatacctcagGGGTATTAGCAGAAGAGGCTTCAAAAATTGCTTCCGCATACAGTGATGTCCTTTCAGCAAAAATTTTGGATGCAGAGCAATGCAAGGAACTGAAAATGGG
















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|254323478|gb|GR835924.1|GR835924
EST:     CATTCTCGGAAGGGAGCTTGTGAATTCTCCGGCTAATGTGCTCACGCCAG                         GGGTATTGGCTGAAGAGGCATCAAAGATTGCTTCAACATATAATGATGTTT
genomic: CATTCTCGGAAGGGAGCTTGTGAATTCTCCGGCTAATGTGCTCACGCCAGgttcatatca ... tttgcctcagGGGTATTGGCTGAAGAGGCATCAAAGATTGCTTCAACATATAATGATGTTT
EST: gi|6454335|gb|AW185018.1|AW185018
EST:     CATTCTCGGAAGGGAGCTTGTGAATTCTCCCGCTAATGTGCTCACGCCCG                         GGGTGTTGGCTGGAGAGGC
genomic: CATTCTCGGAAGGGAGCTTGTGAATTCTCCGGCTAATGTGCTCACGCCAGgttcatatca ... tttgcctcagGGGTATTGGCTGAAGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttcttttgcatttctaggaattgatctgtccttgatgaattatttgcctcagGGGTATTGGCTGAAGAGGCATCAAAGATTGCTTCAACATATAATGATGTTTTTACTGCCAAAATATTAGATGCTGAGCAGTGTAAAGAATTGAAAATGGG
                                             tttgcctc  CT-rich tract
                                  ttgatgaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcaggtagttgaaacatttttacagtttcattgcaacatgtgtgagtttcttttgcatttctaggaattgatctgtccttgatgaattatttgcctcagGGGTATTGGCTGAAGAGGCATCAAAGATTGCTTCAACATATAATGATGTTTTTACTGCCAAAATATTAGATGCTGAGCAGTGTAAAGAATTGAAAATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - -cattgca
- - - - - - - - - - - - - - - - - - - -tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgatg