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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttagctgtttatcagaatgcaatgttttttcaaaatatataatccctacacttcgcttgcatactgacaatttattgctttgcttttgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTCAAGAAGTTGCAGGTGATGTCCGTATGACTGATACCCGTGCAGATGAAGC

Basic information

species Glycine max
transcript GLYMA15G40860.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40860.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0027g00760.t01 (Vitis vinifera), 3'ss of exon 2
atttttagctgtttatcagaatgcaatgttttttcaaaatatataatccctacacttcgcttgcatactgacaatttattgctttgcttttgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTCAAGAAGTTGCAGGTGATGTCCGTATGACTGATACCCGTGCAGATGAAGC
|| ||  | | ||   || | |   ||     ||        ||  |   |  | |||   |   || |   | |||| |||| |  |||||     ||||||| |||||||| || |||||| | ||||||||||||||||||||||||||||||||||| |||||||| || ||||| ||||||||    ||||||||
atgttgtgttcttgtacaaatttacatagaaatttgtgtctaatgttgtgtttaattcttctatttattacaagtttaatgctattgttttgttaaacagGAAAGTCAACCCTCACAGATTCTTTAGTGGCTGCTGCTGGTATTATTGCTCAAGAAGTTGCTGGTGATGTTCGGATGACAGATACCCGCCAGGATGAAGC
















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|209701700|gb|BW673147.1|BW673147
EST:     CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
EST: gi|209720081|gb|BW659468.1|BW659468
EST:     CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
EST: gi|9986901|gb|BE661009.1|BE661009
EST:     CTATAAGCATAATATCCGTAATATGTCTGTCATTGCTCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
EST: gi|209721069|gb|BW666330.1|BW666330
EST:     CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
EST: gi|213591384|gb|DB959898.1|DB959898
EST:     CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
EST: gi|213593027|gb|DB973500.1|DB973500
EST:     CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
EST: gi|213614873|gb|DB956981.1|DB956981
EST:     CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
EST: gi|209719269|gb|BW679811.1|BW679811
EST:     CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
EST: gi|298170535|gb|HO019159.1|HO019159
EST:     CTATAAGCATAATATCCGTAATATGCCTGTCATTGCTCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
EST: gi|254347673|gb|GR853922.1|GR853922
EST:     CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACG                         GAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC
genomic: CTATAAGCATAATATCCGTAATATGTCTGTCATTGCCCATGTTGATCACGgtatggatta ... tgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccctacacttcgcttgcatactgacaatttattgctttgcttttgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTCAAGAAGTTGCAGGTGATGTCCGTATGACTGATACCCGTGCAGATGAAGC
                    tactgac  putative branch site (score: 1)
                                    ctttgctttt  putative PPT
                         acaatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttagctgtttatcagaatgcaatgttttttcaaaatatataatccctacacttcgcttgcatactgacaatttattgctttgcttttgaattgcagGAAAATCAACCCTGACTGATTCTCTTGTGGCTGCTGCTGGTATTATTGCTCAAGAAGTTGCAGGTGATGTCCGTATGACTGATACCCGTGCAGATGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - -gctgttt
- - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - -ccctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgac