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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atataggattatggaagttttatttttaagaagtcacttgtgtaatttatttagttattctatttgtatttctcactcatgatctcttcattttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG

Basic information

species Glycine max
transcript GLYMA04G03290.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 5
atataggattatggaagttttatttttaagaagtcacttgtgtaatttatttagttattctatttgtatttctcactcatgatctcttcattttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG
                  | |      |     |   |   ||||  | |||  ||  |  |        ||| | |  |  | | || |||      |||||||  |  ||| ||    ||  ||  |  | ||  ||||| |||| ||||| ||||| |||||||||||||||||||||||    || ||| || |
-----------------gtctgaccgcagctcattggtaccgtaaggtctttttttggtacaggcaccagtctgatt--ttgtttatttattacac--agATGGTTCGTGACTATAGGACACAACTCATTGACCTTTTGGAAACTGGCAACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGG

upper sequence: GLYMA04G03290.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 5
atataggattatggaagttt---tatttttaagaagtcacttgtg-taatttatttagttattctatttgtatttctcactcatga--tctcttcattttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG
   |  || |   | |   |    ||      |||   ||||||  | | ||  |  || |      |||| | | | |  |||    | | || |  ||||| |||||||  ||||||||| |  ||| |||||  || ||||| |||| ||| | ||||| || ||||||||||||||||||||||||   || || |||||
---tttgactgcagtatcctactcatgcactggaacagacttgttctgaattgctgggtaag---gattgtctcttttaaccattgcttttttttaccttggccagATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG

upper sequence: GLYMA04G03290.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g07610.t01 (Vitis vinifera), 3'ss of exon 4
atataggattatggaagttttatttttaagaagtcacttgtg-taatttatttagttattctatttgtatttctcactcatgatctcttcattt----------tggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG
       | |||   | |  |    |  |  ||  ||||||  | | ||| |  || |    | |||| ||| | |  |||  | | ||  |||          |||| || ||||  ||||||||| |  ||| ||||| ||| ||||| |||| ||| | ||||| || ||||||||||||||||||||| ||   || || |||||
-------aatatcctactcatgcactggaacag--acttgttctgaattactgggtcagg--aattgtcttttttaaccattgtttttttttttattattaccatggccagTTGGTTCGGAACTTTAGAGGACCTCTTCTAAAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAACAAGAGAGCTGTTAAG

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|192334034|gb|FK026191.1|FK026191
EST:     CTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAG                         ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
genomic: CTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAGgtattttaat ... ttttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
EST: gi|58020362|gb|CX707104.1|CX707104
EST:     TAGCCATACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAG                         ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
genomic: TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAGgtattttaat ... ttttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
EST: gi|208192105|gb|GD990639.1|GD990639
EST:     TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAG                         ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
genomic: TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAGgtattttaat ... ttttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
EST: gi|58016809|gb|CX703551.1|CX703551
EST:     TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAG                         ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
genomic: TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAGgtattttaat ... ttttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
EST: gi|192323065|gb|FK016316.1|FK016316
EST:     TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAG                         ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
genomic: TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAGgtattttaat ... ttttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
EST: gi|192326921|gb|FK015148.1|FK015148
EST:     TAGCCAAACAGGAAAGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAG                         ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCT
genomic: TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAGgtattttaat ... ttttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCT
EST: gi|10848246|gb|BF070781.1|BF070781
EST:     TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAG                         ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC
genomic: TAGCCAAACAGGAAGGCCTTCTTGTTTCCTTGGATTTGGCCAGTTTTGAGgtattttaat ... ttttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttagttattctatttgtatttctcactcatgatctcttcattttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG
                        ttctcac  putative branch site (score: 2)
                                     tctcttcatttt  putative PPT
     ttagttattctatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atataggattatggaagttttatttttaagaagtcacttgtgtaatttatttagttattctatttgtatttctcactcatgatctcttcattttggcaagATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - -acttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttca