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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaagtttatttgctgttatatctagctttcggaaaaaaataaacttgtctgacttgagattatgaggtcaatagagtaattctttttgaattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG

Basic information

species Glycine max
transcript GLYMA0048S00290.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 8
-----ataaagtttatttgctgttatatctagctttcggaaaaaaataaacttgtctgactt-----gagattatgaggtcaatagagtaattctttttgaa-----ttttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG
      |   ||| |  ||    |  |  ||    | | |    | ||| ||||| |  |||      | | | | |  |  ||      || |  |   |      |||| ||||| |||||||| |||||||| || ||| | ||||||||||| |||||||| || || |||| ||| |  |||
gtaagtttctgttcacatgtcagtccagataatcatagcattgtactaagcttgtatttcttttttcaatactgttatattgatgctcacataccctgcaataccttttttccagGTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG

upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 8
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 8
ataaagtttatttgctgttatatctagctttcggaaaaaaataaacttgtctgacttgagattatgaggtcaatagagtaattctttttgaattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG
    ||| |  |   | | ||   | | | |     |  | |   | | |   |  |  | ||| | | |   ||     ||| | |||   || |  |||||||||| |||||||||||||||||||| ||||| ||||| ||||||||  | ||||||||||| || |||
-gtgagtgtcctgcttctaatgaattgatattttttattagtgggcgttttgaaactctgctta-gtgattgtta-----attttgttttgtttgtgaagGTATGGTCTGCACCTAATTACTGTTACCGCTGTGGGAATGTCGCTTCTATATTGAGTTTCAATGACAACATG

upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 8
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 8
ataaagtttatttgctgttatatctagctttcggaaaaaaataaacttgtctgacttgagattatgaggtcaatagagtaattctttttgaattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG
    |  |   |||||    |||     ||| ||| |     ||   |      ||||    | |    ||  |    | ||| ||||||     || |||| ||||| || ||||||||||| ||||||||||| ||||| ||||||||  | ||||||||||| || |||
--gtaagtgccttgcttccttatgatcattttggatagttggaagtataatctgcttggtgatgtttcttctct----ttattttttttg-----taaagGTGTGGTCTGCGCCTAATTACTGCTACCGTTGTGGGAATGTGGCTTCTATATTGAGTTTCAATGACAACATG

upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 8
ataaagtttatttgctgttatatctagctttcggaaaaaaataaacttgtctgacttgagattatgaggtcaatagagtaattctttttgaattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG
          |  | |  | ||      ||| | |      |   | |   |   || |       |  | |||||  | ||||||   || |||| ||||| ||||| ||||| || ||||||||||||||||| ||||| ||||| ||  | || |||||||| ||||||
---------gtaagattctgta---gatttttgcagttgttttgtcatcgatagttttaaccatcaatattaatagtttgattctt---gactttttcagGTCTGGTCTGCACCAAACTACTGTTACCGTTGTGGGAATGTGGCTTCCATATTGAGCTTCAATGAGAATATG

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|254340656|gb|GR854384.1|GR854384
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|151410851|gb|EV280666.1|EV280666
EST:     TCGTTCAAGAAG-TCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|213611336|gb|DB983956.1|DB983956
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|193346878|gb|FK310146.1|FK310146
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|207746865|gb|GD721124.1|GD721124
EST:     CAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: CAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|31464149|gb|CD406177.1|CD406177
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAATGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|254340657|gb|GR854385.1|GR854385
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|209728248|gb|BW651683.1|BW651683
EST:     TCGTTCAAGAATGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|213593175|gb|DB975366.1|DB975366
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|16345163|gb|BI970758.1|BI970758
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|31473271|gb|CD415284.1|CD415284
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|254337376|gb|GR849329.1|GR849329
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
EST: gi|5753202|gb|AI960489.1|AI960489
EST:     TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT                         GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT
genomic: TCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACTgtaagtatct ... aattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtctgacttgagattatgaggtcaatagagtaattctttttgaattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG
   gtctgac  putative branch site (score: 3)
                               agtaattctttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaagtttatttgctgttatatctagctttcggaaaaaaataaacttgtctgacttgagattatgaggtcaatagagtaattctttttgaattttacagGTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG

- - - - - - tgctgtt
- - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg