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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagtagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC

Basic information

species Glycine max
transcript GLYMA10G42940.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------------------------aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagt--agctaatccctaaaa----tgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC
                                                                              ||  | |||   |  || | | |      |    ||    |||||  | || ||   ||||            || ||||    |   |    | |  | |||||||||||||| || ||||||||||| ||||| ||||| ||||| || || ||||| ||||||||||| ||||||||||| ||||| || ||||| ||  
gtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggctactctgt-ttacagGCAAATGATCCCACCATTGAACGTATCATCACCCCTCGAATTGCACTGACAACTGCAGAATATTTGGCATATGAATGTGGGAAGCACGTGCTTGTCATCT

upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 8
---aaagcaaaatttaaatgaggcttt-ttgatttcctgacttgcatgaagtagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC
       |      |  || | | |      | |   |        |||  ||   | |   ||  |     | ||  |||       ||      |  | ||||| |||||||| || ||||||||||||||||| ||||| |||||||| || || || ||||||||||| ||||||||||| |||||||| ||||| ||  
ctatcctctggccctgcataacgatgagccaaatatattctacatgtgacataatcagtgtatagcacagcatatttttaacaccttgat----cctcttacagGCTAATGATCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCAGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTCATCT

upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 8
--aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagtagctaatccctaaaatgttctcttgctaatg--tgaatatgtgatttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC
     ||| |   |||    |      | |||| || | ||   |||  ||  || |   ||| |     | ||  |||    | |||      | |  | ||||| || || || || ||||||||||||||||| ||||| |||||||| || || || ||||||||||| ||||||||||| |||||||| ||||| ||  
cccctgcaca-cataatcatgagccaatcattttctaaatt---tgacataattagtgtataatacagcatatttttaacacctcaattctctctgttttacagGCTAACGACCCCACCATTGAACGTATTATCACCCCTCGGATTGCTCTAACAACAGCGGAATATTTGGCATATGAATGTGGGAAGCATGTACTTGTTATCT

upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 9
aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagtagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttac-tgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC
            || |   ||  |   | | |  ||| | | ||||| |  |  |   |  |||||| |  ||    | |     | || ||| |   |||||||| || || || ||||| ||||| |||||||||||||| || ||||| |||||||| || ||||| |||||||||||||||||||| ||||| || |
----------gcaagtctcgcaatcacactaca-gacat-cttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACAACTGCTGAGTACTTGGCATATGAATGTGGCAAGCATGTCCTTGTCATTC

upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 8
-----aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagt----------agctaatccctaaaatgttctcttgctaatg--tgaatatgtgatttactg--cagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC
      |    ||||| | ||   | | |||  | |  |   | |  | || |          | | |  |   | |||  |    |   |||   |    || || |  | ||  ||||| || || || || |||||||| || ||||||||||| |||||||| || |||||||||||||| || |||||||||||||| ||||||||||| ||||
gtatttatattaaattaatatagtggtatttattattgtttgtggtgtaaattctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacagGCCAACGACCCCACCATTGAACGCATCATCACTCCTCGAATTGCTCTCACCACTGCTGAATATTTAGCATATGAATGTGGCAAACATGTTCTTGTCATAC

upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 7
aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagtagctaatccctaaaatgttctcttgctaa-tgtgaatatgtgatttact-gcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC
||| |||  ||         | | ||  | |  |  || | |  |  |   |  |   |   || ||       ||| |  |||| | |  |   || |||||| |||||||| || |||||||| |||||||||||||| || || ||||||||||||||||| |  |||||||||||||| |||||||| || || || |
aaatcaatgttcttccattccctctt--tctttttcctcgaacaatttctgtggtaagtcttatatttagaatttaagttcgaatctctcttgggcttgcagGCTAATGATCCAACGATTGAACGGATTATCACTCCTCGAATCGCCCTTACTACTGCTGAATACTACGCTTATGAATGTGGGAAGCATGTCCTGGTCATCC

upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 8
aaagcaaaatttaaatgaggctttttgatttc----ctgacttgcatgaagtagc-taatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC
    ||   ||  ||     || || | | ||       | || | | ||  ||        | || || |  | ||   | | ||||| | |  |    ||||||| |||||||| |||||||| ||||| ||||||||||| ||||| || ||||||||||||||||  |||||||| ||||| ||||||||  | || ||||
----catgtttccaaccct-ctcttcgttctcggtatcaaatttcgtaaatcagtgctggaacgaacatttcgtgttttaattttgaatttatactgatttgcagGCTAATGATCCAACAATTGAGCGTATCATCACTCCTCGAATTGCACTCACTACTGCTGAATATTATGCTTATGAGTGTGGGAAGCATGTGTTGGTCATAC

upper sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------------------------------------------------aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagtagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC
                                                                                                           |  |   |   |    |   |  |  | | | ||  ||   |        |||   ||  ||| || | ||   |  ||     || | |||    ||||| |||||||| |||||||| ||||||||||| ||||| ||||| ||||| |||||||| || |  |||||||| ||||| ||||| ||||| || || |
gtatgtacatcttcagttttcttttatcgtcgattttcaccacatttttggattatatatggaacttcatccagtttcttttcgtaatggaagagtcgtctgttttgagacttcacaaagtcaattttcctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgt---cttgggcttt----cagGCTAATGATCCAACAATTGAGCGTATTATCACACCTCGAATTGCACTTACAACTGCTGAGTACTACGCTTATGAGTGTGGAAAGCACGTTCTGGTCATCC

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|19452473|gb|BM953883.1|BM953883
EST:     CAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: CAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|120533616|gb|EH261749.1|EH261749
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTTCTTAAATTG                         TCCAATGATCCTACAATTGAACGTATTATCATTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16278890|gb|BI943147.1|BI943147
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|193355970|gb|FK322627.1|FK322627
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16277797|gb|BI942567.1|BI942567
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTATAC
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCT-TAC
EST: gi|16283207|gb|BI945427.1|BI945427
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|193430619|gb|FK396393.1|FK396393
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16278507|gb|BI942940.1|BI942940
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaacccttt ... tttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC
                          tgctaat  putative branch site (score: 2)
             taaaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagcaaaatttaaatgaggctttttgatttcctgacttgcatgaagtagctaatccctaaaatgttctcttgctaatgtgaatatgtgatttactgcagGCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACTACTGCTGAATATTTGGCTTATGAATGTGGCAAGCATGTTCTTGTGATAC

-aagcaaaa
- - - - - - - atgaggc
- - - - - - - - - - - - - - - -cctgact
- - - - - - - - - - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctaaa