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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatactttgctctactcggttcttgtcttggtttctcggaattgctttgccattacttttatgcagtacgcaggctaacttttcttttcatgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGCTAAATACT

Basic information

species Glycine max
transcript GLYMA04G42900.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g59550.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------tatactttgctctactcggttcttgtcttggtttctcggaattgctttgccattacttttatgcagtacgcaggcta--acttttcttttcatgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGCTAAATACT
                                                         || | ||     ||||   |  |   || | ||| |  |  | ||  ||  |  |      |  |  | |     ||  || |||| ||   | |   ||||||| |||||||| || ||||||||||| ||||| ||||||||  |||| || || ||  |||||||||||||    ||  |  ||   ||| |  | || 
gtaggtgctcatcttatggcgggtgtaatgactggtgctttacttctgctgtgatcttacagtt-ataatactgtatggtaaactggatttttttg--tcgccgtgttaccagcaaagtaaatcatgttatttatgacgtttccttgtgttttcttcagCATTAACACAGTGTACTACATGGCACCCTTTGCCACCATGATACTGGCTCTACCAGCAGTGTTACTTGAAGGAGGCGGTGTGGTTACCTGGTTCTACACA

upper sequence: GLYMA04G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g02970.t01 (Vitis vinifera), 3'ss of exon 3
----tatactttgctctactcggttcttgtcttggtttctcggaattgctttgccattacttttatgcagtacgcaggctaacttttcttttcatgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGCTAAATACT
    ||    ||     |  |  |  ||   ||  ||| |     ||   |||   ||    | || |    |    | | | |||| ||| |       | |||||||||||||| || ||||||||||||||||||||||||||||||||  | || || ||| ||||||||||   |||  |  | || ||| |  | |||
tgtttaagtattatagaatacattattttattttctttttgtatgttttattgatgttcaactcatacttgtcttgtgattatttttgtttac----cctttagCATAAACACAGTGTACTACATGGCACCTTTTGCAACCATGATCTTGGCAGTGCCAGCTATGGTACTTGAAGGTCCTGGTGTTATAGATTGGTTTCAAACT
















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|51341561|gb|CO982878.1|CO982878
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCT
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtacggtctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCT
EST: gi|192296166|gb|FG989751.1|FG989751
EST:     ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCAC
genomic: ACAAAGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtacggtctt ... tgtatctcagCATAAACACAGTTTATTACATGGCAC
EST: gi|20814095|gb|BQ298573.1|BQ298573
EST:     CTCTTCTGCATGGATACAAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCT
genomic: CTCTTCTGCATGGATACAAATTTGACAGgtacggtctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCT
EST: gi|31307609|gb|CD392812.1|CD392812
EST:     AGACTATTCTTGCAGAATCTCTTCTGCATGGATACGAATTTGACAG                         CATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCT
genomic: AGACTATTCTTGCAGAATCTCTTCTGCATGGATACAAATTTGACAGgtacggtctt ... tgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgccattacttttatgcagtacgcaggctaacttttcttttcatgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGCTAAATACT
                           ggctaac  putative branch site (score: 2)
                                 cttttcttttcatgt  CT-rich tract
      attacttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatactttgctctactcggttcttgtcttggtttctcggaattgctttgccattacttttatgcagtacgcaggctaacttttcttttcatgtatctcagCATAAACACAGTTTATTACATGGCACCTTTTGCAACCATGATCTTGGCGCTTCCTGCCATGTTACTTGAAGGCAATGGAATCCTTGAATGGCTAAATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - -tgtcttg
- - - - - - - - - - - - - - - - - - - - - - ctttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacgca