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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttattttgtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattctttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA

Basic information

species Glycine max
transcript GLYMA09G03470.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 2
tttattttgtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattc--tttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA
   | | ||||     |  | ||      |||||      |   |   ||  ||||  ||  | ||  |  || ||||     |   |  | |||||| |||   |  || ||||| || ||| | ||| |||||||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||||||||| ||||
-aaaatgtgtctacattcctgttgcattcatgcttgaccaga-aagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttctccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA

upper sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4
tttattttgtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattc--tttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA
  ||| | |||     |  | ||      |||||      |   |   ||  ||||  ||  | ||  |  || ||||     |   |  | |||||  |||   |  || ||||| || ||| | ||| |||||||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||||||||| ||||
aatatgt-gtctaaattcctgttgcattcatgcttgaccaga-aagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA

upper sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 3
tttattttgtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattct---ttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA
 |||||| | | |   | || |       || ||| |       |||  |       |  ||    |  |||||||| | |   |   |  |   |||| |||   | ||| || || || ||| ||||| |||| ||||| ||||| |||||||||||||| ||||| |||||||| ||||| |||||||||||||| ||||
-ttattt-gcctttcctcatttccattgtat-ctattaaccagaaaatgaatgaggtgcctgtggatgcattttgaaatgtgactgttttctttgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGAGTTCTTCACCGAGATTTGAAACCTCAGAACTTGTTGATAGATCGGCGTA

upper sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
-------tttatttt-gtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattctttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA
        | ||||   | ||   | |||    | | |||   | |  |||| |  | |  ||  ||      | |||| |  || | |||  |    |||||| |||   | ||| || || || |||   ||  |||| ||||| ||||| ||||||||||||||||||||||||||||| || || || ||||||||||| || |
ccctttcctcatttccattatatctcataacctgaaaatg---aatgaggtgcaggtgcttgtgggtgcattctgaaatgt--aactattttct---tctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA

upper sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 4
tttattttgtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattctttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA
     |  ||  |  |  |  ||||| |     | || |  |||   | ||    || |    ||       |   |    || ||    || | | ||||  |  ||||| || |||||| |||| ||||| || || || || ||||| ||||| ||||| ||  |||| ||||||||||||||||| |||||||| |
----gtgagtgctaagaaactttaggcattgttttatatatgtgcttaaactcaatactcaatataagctgatcagagctgttcatc-cactattttcagACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATCTGAAGCCACAGAATTTGTTGATTGATCGCCGCA

upper sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
tttattttgtc-atgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattctt-taatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA
||| |  |||| ||   ||| ||||     ||  | ||||  | | | || |  |    |   | |   |  |  |  ||||   | |       | |||||||||||||  |||| |||||| |||| |||||||| |||||||| ||||| |||||||||||||| ||||| || ||||| ||  | |||||||| ||||
tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggtgcga--tggggcttctgacacttgagtcctttgcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTA

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|120532704|gb|EH260837.1|EH260837
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATG-TCCTTTATCAAA-TCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|192309059|gb|FK001835.1|FK001835
EST:     AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATG-TCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|192312501|gb|FK004987.1|FK004987
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|298169145|gb|HO020505.1|HO020505
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|151396909|gb|EV266782.1|EV266782
EST:     NNCACATGGATTCATCTCCAGAGTTCGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|298190796|gb|HO032917.1|HO032917
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCCGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|192295604|gb|FG988178.1|FG988178
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|6073117|gb|AW102504.1|AW102504
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|298178270|gb|HO024005.1|HO024005
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|298182098|gb|HO026273.1|HO026273
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|192330928|gb|FK023101.1|FK023101
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTGCTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|9204181|gb|BE330405.1|BE330405
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|192312081|gb|FK003858.1|FK003858
EST:     CACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGTAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: CACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|213591734|gb|DB973355.1|DB973355
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|24136151|gb|BU926661.1|BU926661
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|151394972|gb|EV264843.1|EV264843
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|13562876|gb|BG551096.1|BG551096
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|151409597|gb|EV279405.1|EV279405
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|192309058|gb|FK001834.1|FK001834
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTTGCTTACTGTCATTCACATAG
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCA-TTGCTTACTGTCATTCACATAG
EST: gi|192312486|gb|FK004986.1|FK004986
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|15813934|gb|BI786209.1|BI786209
EST:     NNCACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
EST: gi|192300023|gb|FG991841.1|FG991841
EST:     AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAG                         ATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA
genomic: AACACATGGATTCATCTCCAGAGTTTGTGAAAGATCCGCGGCAAGTAAAGgtgagcgacc ... ctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataccagttagtttggatttaaattttgaattctttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA
                                  ctttaat  putative branch site (score: 4)
                                           tcctttctgc  putative PPT
             tttggatttaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttattttgtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattctttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA

- - - -tgtcatg
- - - - - - - - - - - - - - gatgcta
- - - - - - - - - - - - - - - - - - -tttggtg
- - - - - - - - - - - - - - - - - - - - - - aaaatacc