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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA

Basic information

species Glycine max
transcript GLYMA08G18240.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 5
ttccatatttttatgagtatc-ctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
||  ||   |   ||  |||   |||||||     | |   |  | |||   ||| | |   ||   ||| |||   |   ||| | |    | |    |||| ||||| ||||| ||||||||||||||||||||||| || |||||||||||||| |||||  | ||||| || |||||||||||||||||||| ||||
ttttatgggtcactgcatattgttttttattttttgatctctcgaagtcaataatgagaaaatattacatatgta-atacatacctatttcttcttaacagGGGCATGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTTTGATAGCAGCCAATGAAAGCTGCCCACAACCCCAAA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 5
--ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
  |   ||  | | ||    |    ||||||  ||   |||    |||| |    | | ||  |   | |    |  |   |||| | |    | |    ||||||| |||||||| |||||||| |||||||||||||| || |||||||||||||| ||||| || ||||| || |||||||| ||||||||||| || |
tgtaaaatgctatcatttcaacttcttttatgggccactaagactaggtattggtttacat--ttgttgaagcctgagaaattacctatttcctcttaacagGGACACGATATTCTCATGGCTACGATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTCTGATAGCAGCAAATGAAAGTTGCCCACAACCCCAGA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttct----gtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
    | ||  ||||    ||   ||| | |      |   ||  | ||    || | ||   |||| ||| || |||||  ||  | || || ||      |||||||| || ||||| ||||||||||||||||||||||| || ||||||||||||||  | ||  | || || || |||||||| || ||||| || || |
---aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataatt-gtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 5
------ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
      ||  || |||  |  |      | |   | |  ||  |   |   ||||   |  ||||    |||  | |||||     ||| | | |   ||   |||||||| || ||||| ||||||||||||||||||||||| || ||||||||||||||  | ||  | || || || |||||||| || ||||| || || |
gaataattgtatgtttcaacaacacctatctccttgaatagagatgaatttgtctaacaggaaat----aattgtatgtttaacaatacctattc--cttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCCCAGA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 4
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgt-----agGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
                      | || || ||     | |||||  |   |  |||||     || |||| | |   | | |||       ||| | |     |||||||||||||||||||||| |||||||| ||||||||||||||| ||||||| || || || || || |||||||| || || || |||||||||||||
---------------------gtattaatgagttta-atttacactttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
           ||| |      |||| | |      || ||  |  |||    |  ||   |     || ||||  |      ||||     ||   |||||||| ||||| || ||||| |||||||| ||||||||||| || |||||||| || || ||| |||| ||||| ||||| |  || |||||||||||||
----------gtataaaatgagttttaacac-----tatttctaaatcttttgt--aaccattttctatatgttaatgaggtgttttgtgtgttgattagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 5
-ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
     |   ||    ||| |   ||  |  | |     |  |   | | | |       | ||  ||  ||  |   | | | ||| | | |||  |  |||| || |||||||| ||||| |||||||||||||||||||| ||||||||||| ||  | ||  | || ||||| |||||||  || |||||||||||||
gagtgagggttgatggagaagtattcattgatgtttccatcttttgcttttcttatctctacttcattcttgttgaatgtattcttgttctattctt-cagGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAGCCATCATGGATGGTGCACTACTTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctg---tagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
    |    || |     |   | |  ||   ||||   ||| | | ||       | | |   |   ||| ||   |||| ||||| || |||      ||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| || || || || |||||||| || |||||||| ||||| || ||||
-ctaaagacttgactttaaggttctggatgtccaggc--ttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttc---tgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
     |   |||| || | |   | |   | ||    |      ||||| |  || | || |   |  ||| | |||||||  |||| ||  |||   | ||||| ||||||||||| ||||||||||||||||||||||| ||||| |||||||| || || || || |||||||| ||||||||||| ||||| || ||||
gaaggtggctttaagattctggatgtc-caggcctaaatgcctgggtctactgtctagtgatt--ttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 3'ss of exon 4
ttccatatttttatgagtatc-ctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaattt--ctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
    ||     ||     ||| |||  | | ||    ||     ||   | |  ||   | ||   |  |      | ||  | | ||    |||   || ||||||| |||||||| |||||||| |||||||||||||| || || |||||||| || || ||  | || ||    ||||| || ||||| || || ||||
---aattcgactacacacatcacttaatctgagggcttatgggaagcggtactttcgtgttcttgtttttaatccggattgaaatgtttgtgtttgtttgcagGGACACGATATTCTCATGGCTACTATGCTTAATGGAGCTGCTATTATGGATGGTGCTTTACTTTTGATTGCCAGCAATGAGAGTTGCCCCCAGCCCCAAA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
                                           | ||      |    | |    || | |   |||| |||     | ||    |  |||||||||||||||| |||||||| ||||||||||| || || |||||||| || || |||||  | || ||    || ||||||||||| || || ||||
-----------------------------------------gtaagttcgtcgtagttttcgttttcttctagctgttctta-----cgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA

upper sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ26525 (Selaginella moellendorffii), 3'ss of exon 3
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
                                           | ||      ||  |   |   |  | |  | | ||||   || | ||    |  |||||||||||||||| |||||||| ||||||||||| || || |||||||| || || |||||  | || ||    || |||||||| || || || ||||
-----------------------------------------gtaagttct---tcgtagttttcgttttcttctagctttt--cttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGTCCGCAGCCGCAAA

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|254316161|gb|GR825970.1|GR825970
EST:     AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|19935170|gb|BQ080200.1|BQ080200
EST:     AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|17023024|gb|BM094058.1|BM094058
EST:     AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|7478465|gb|AW666276.1|AW666276
EST:     AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|209708854|gb|BW673890.1|BW673890
EST:     AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|23727056|gb|BU761544.1|BU761544
EST:     AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|18692825|gb|BM521673.1|BM521673
EST:     AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|15663764|gb|BI701135.1|BI701135
EST:     AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTAAGGCATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
             tgctaaa  putative branch site (score: 2)
                                     cttttccaatttct  putative PPT
                taaatcatttgtttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - -ccaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcta