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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttgtgtgctagcacatgaatggtcgcttcagttacttagtcttttggggatcttttatccaagtttcttaacagtagtatgctttttcaatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGAGAAGTCAATAATGTGAAGACAGAATTG

Basic information

species Glycine max
transcript GLYMA17G15720.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G15720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0309g00040.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------------------ttgttgtgtgc-tagcacatgaatggtcgcttca--gttacttagtcttttggggatcttttatccaagtttc---ttaacagtagtatgctttt-tcaatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAA---CCTTGCAAGAAGAGAAGTCAATAATGTGAAGACAGAATTG
                                                              ||||  | |    |   |  ||| |   |       |||| |||    |     |   || | ||  | |||    | || |||  | | ||  | ||||| |||| ||||||||||||||||||||||| || |||||| || |   ||||||||||| |||||| || ||||||||| |||     
gtttcttcttgaccagtactttttattgctctaagatattgtgtatcttttgttctcttgctttgtcttttttacaaggctcgaaagagagtcatgatgttaattaaatgtccaaaggcattct-tcagattttaacatgaaaagTCATGTCCTCCTATCAATCTGCATCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGATCACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAG-----

upper sequence: GLYMA17G15720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0309g00080.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------ttgttgtgtgctagcacatgaatggtcgcttca-gttacttagtcttttggggatcttttatccaagtttc---ttaacagtagtatgctttt-tcaatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGAGAAGTCAATAATGTGAAGACAGAATTG
                                                                 | || | | | ||      ||  ||  | | | |||| |||   ||     |   |||| || || |||    | || |||  | | ||  | ||||| |||| |||||||||||| |||||||||| || |||||| || |||||||||||| |||||| || ||||||||| |||| |  
gtttcttctttaccagtactttttattgctctaagctattgtgtatcttttgttctcttgctttgtcttttttacaaggctcgaaagagtgtcatgatgttaattaaatttccaaaggaatttt-tcaaattttaagatgaaaagTCATGTCCTCCTATCAATCTGCATCCAATTGCAAGGCTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGT--

upper sequence: GLYMA17G15720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s1355g00010.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------------------------------ttgttgtgtgctagcacatgaatggtcgcttcagttacttagtcttttggggatcttttatccaagtttcttaacagtagtatgctttttcaa---tttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGAGAAGTCAATAATGTGAAGACAGAATTG
                                                         ||| | ||| ||     |  |  | |||    |||  | |  | ||      || |   |    | | |    |   ||  |||     |||    | |||||||||||||||||||||||||||| || |||||| || |||||||||||| |||||| || ||||||||| |||| |||
gtttcttcttgactagtactttttattgctctaagctactgcgtatctgttgttctcttgctttgt-cttttttacaag-gctcgaaagagtgtcatgatgttaattaaatgtccaaagtcattcttcagattttaacatgaaaagtcatgtctctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGTTG

upper sequence: GLYMA17G15720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0204g00220.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------------ttgttgtgtgctagcacatgaatggtcgcttca-gttacttagtcttttggggatcttttatccaagtttc---ttaacagtagtatgctttt-tcaatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGAGAAGTCAATAATGTGAAGACAGAATTG
                                                                 | || | | | ||      ||  ||  | | | |||| |||    |     | || ||  ||  | |||    | || |||  | | ||  | ||||| |||||||||||||||||||||||||||| || |||||| || |||||||||||| |||||| || ||||||||| |||| |||
gtttcttcttgactagtactttttattgctctaagctactgcgtatctgttgttctcttgctttgtcttttttacaaggctcgaaagagtgtcatgatgttaattaaatgtccaaag-tcattcttcagattttaacatgaaaagtcatgtcctcctatcaatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGTTG

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|58015347|gb|CX702089.1|CX702089
EST:     CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
EST: gi|120533475|gb|EH261608.1|EH261608
EST:     CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
EST: gi|120533390|gb|EH261523.1|EH261523
EST:     CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACA
EST: gi|10238654|gb|BE807542.1|BE807542
EST:     CAAAGGGTAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
EST: gi|13562908|gb|BG551128.1|BG551128
EST:     CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCA
EST: gi|9565026|gb|BE474535.1|BE474535
EST:     CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
EST: gi|57574344|gb|CX547319.1|CX547319
EST:     CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
EST: gi|51343450|gb|CO984183.1|CO984183
EST:     CAAAGGGTAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
EST: gi|58014949|gb|CX701691.1|CX701691
EST:     CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
EST: gi|58022215|gb|CX708956.1|CX708956
EST:     CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
EST: gi|151401250|gb|EV271064.1|EV271064
EST:     CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAG                         CCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA
genomic: CAAAGGGAAACCGTTCTGCTTTGCCATCATCAACAATAATGATAAGACAGgtttgttccc ... caatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggggatcttttatccaagtttcttaacagtagtatgctttttcaatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGAGAAGTCAATAATGTGAAGACAGAATTG
                       tcttaac  putative branch site (score: 2)
                                     tgctttttc  putative PPT
                                        tttttcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttgtgtgctagcacatgaatggtcgcttcagttacttagtcttttggggatcttttatccaagtttcttaacagtagtatgctttttcaatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGAGAAGTCAATAATGTGAAGACAGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - tgtgtgc
- - - - - - - - catgaat
- - - - - - - - - - - - - -gcttcag
- - - - - - - - - - - - - - - - - - - - - - -tttgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgct